Created
January 17, 2017 08:45
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OpenMS workflow, label free quantification, Sciex TripleTOF 6600 (centroid mode), 11/01/2017
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
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| <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> | |
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(K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| <ITEMLIST name="variable_modifications" type="string" description="Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| <ITEM name="missed_cleavages" value="1" type="int" description="Number of possible cleavage sites missed by the enzyme" required="false" advanced="false" /> | |
| <ITEM name="minimum_fragment_mz" value="150" type="double" description="Minimum fragment mz" required="false" advanced="false" /> | |
| <ITEM name="cleavage_site" value="Trypsin" type="string" description="The enzyme used for peptide digestion." required="false" advanced="false" restrictions="Trypsin/P,glutamyl endopeptidase,unspecific cleavage,PepsinA,Arg-C,Formic_acid,V8-DE,Asp-N_ambic,CNBr,2-iodobenzoate,Trypsin,Chymotrypsin,Asp-N,Lys-C,V8-E,leukocyte elastase,TrypChymo,Lys-C/P" /> | |
| <ITEM name="output_results" value="all" type="string" description="Which hits should be reported. All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)" required="false" advanced="false" restrictions="all,valid,stochastic" /> | |
| <ITEM name="max_valid_expect" value="0.1" type="double" description="Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic'" required="false" advanced="false" /> | |
| <ITEM name="refinement" value="false" type="string" description="Enable the refinement. For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="use_noise_suppression" value="false" type="string" description="Enable the use of the noise suppression routines." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="semi_cleavage" value="false" type="string" description="If set, both termini must NOT follow the cutting rule. For most applications it is NOT recommended to set this flag." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="PeptideIndexer" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="30" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="250" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input idXML file containing the identifications." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fasta" value="" type="input-file" description="Input sequence database in FASTA format. Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'" required="true" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="out" value="" type="output-file" description="Output idXML file." required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="decoy_string" value="dec_" type="string" description="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins." required="false" advanced="false" /> | |
| <ITEM name="decoy_string_position" value="prefix" type="string" description="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" required="false" advanced="false" restrictions="prefix,suffix" /> | |
| <ITEM name="missing_decoy_action" value="warn" type="string" description="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message)" required="false" advanced="false" restrictions="error,warn" /> | |
| <ITEM name="write_protein_sequence" value="true" type="string" description="If set, the protein sequences are stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="write_protein_description" value="true" type="string" description="If set, the protein description is stored as well." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_proteins" value="false" type="string" description="If set, protein hits which are not referenced by any peptide are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="allow_unmatched" value="true" type="string" description="If set, unmatched peptide sequences are allowed. By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="full_tolerant_search" value="false" type="string" description="If set, all peptide sequences are matched using tolerant search. Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="aaa_max" value="4" type="int" description="[tolerant search only] Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs. AAAs are 'B', 'Z' and 'X'" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mismatches_max" value="0" type="int" description="[tolerant search only] Maximal number of real mismatches (will be used after checking for ambiguous AA's (see 'aaa_max' option). In general this param should only be changed if you want to look for other potential origins of a peptide which might have unknown SNPs or the like." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="IL_equivalent" value="false" type="string" description="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="filter_aaa_proteins" value="false" type="string" description="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs. This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="4" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="enzyme" description=""> | |
| <ITEM name="name" value="Trypsin/P" type="string" description="Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)." required="false" advanced="false" restrictions="Formic_acid,Asp-N,Asp-N_ambic,Chymotrypsin,Trypsin,Arg-C,CNBr,2-iodobenzoate,unspecific cleavage,no cleavage,V8-DE,Trypsin/P,PepsinA,glutamyl endopeptidase,Lys-C/P,proline endopeptidase,Lys-C,V8-E,TrypChymo,leukocyte elastase" /> | |
| <ITEM name="specificity" value="full" type="string" description="Specificity of the enzyme.#br# 'full': both internal cleavage sites must match.#br# 'semi': one of two internal cleavage sites must match.#br# 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here" required="false" advanced="false" restrictions="full,semi,none" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDPosteriorErrorProbability" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-250" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="490" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out_plot" value="" type="output-file" description="txt file (if gnuplot is available, a corresponding PDF will be created as well.)" required="false" advanced="false" supported_formats="*.txt" /> | |
| <ITEM name="split_charge" value="false" type="string" description="The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="top_hits_only" value="false" type="string" description="If set only the top hits of every PeptideIdentification will be used" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="fdr_for_targets_smaller" value="0.05" type="double" description="Only used, when top_hits_only set. Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run." required="false" advanced="true" /> | |
| <ITEM name="ignore_bad_data" value="false" type="string" description="If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="prob_correct" value="false" type="string" description="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="fit_algorithm" description="Algorithm parameter subsection"> | |
| <ITEM name="number_of_bins" value="100" type="int" description="Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized" required="false" advanced="true" /> | |
| <ITEM name="incorrectly_assigned" value="Gumbel" type="string" description="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used." required="false" advanced="true" restrictions="Gumbel,Gauss" /> | |
| <ITEM name="max_nr_iterations" value="1000" type="int" description="Bounds the number of iterations for the EM algorithm when convergence is slow." required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FalseDiscoveryRate" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="150" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="470" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Identification input file containing a search against a concatenated sequence database. Either specify '-in' alone or 'in_target' together with 'in_decoy' as input." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="in_target" value="" type="input-file" description="Identification input file containing a search against a target-only database." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="in_decoy" value="" type="input-file" description="Identification input file containing a search against a decoy-only database." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Identification output with annotated FDR" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="proteins_only" value="false" type="string" description="If set only the FDR on protein level is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="peptides_only" value="false" type="string" description="If set only the FDR on peptide (PSM) level is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameter section for the FDR calculation algorithm"> | |
| <ITEM name="no_qvalues" value="false" type="string" description="If 'true' strict FDRs will be calculated instead of q-values (the default)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="use_all_hits" value="false" type="string" description="If 'true' not only the first hit, but all are used (peptides only)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="split_charge_variants" value="false" type="string" description="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="treat_runs_separately" value="false" type="string" description="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="add_decoy_peptides" value="false" type="string" description="If 'true' decoy peptides will be written to output file, too. The q-value is set to the closest target score." required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-250" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="650" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDMerger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-230" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="890" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="input-file" description="Input files separated by blanks" required="true" advanced="false" supported_formats="*.idXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="add_to" value="" type="input-file" description="Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="annotate_file_origin" value="false" type="string" description="Store the original filename in each protein/peptide identification (meta value: file_origin)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="pepxml_protxml" value="false" type="string" description="Merge idXML files derived from a pepXML and corresponding protXML file.#br#Exactly two input files are expected in this case. Not compatible with 'add_to'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FidoAdapter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-230" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1090" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input: identification results" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output: identification results with scored/grouped proteins" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="fido_executable" value="Fido" type="input-file" description="Path to the Fido executable to use; may be empty if the executable is globally available." required="true" advanced="false" /> | |
| <ITEM name="fidocp_executable" value="FidoChooseParameters" type="input-file" description="Path to the FidoChooseParameters executable to use; may be empty if the executable is globally available." required="true" advanced="false" /> | |
| <ITEM name="separate_runs" value="false" type="string" description="Process multiple protein identification runs in the input separately, don't merge them. Merging results in loss of descriptive information of the single protein identification runs." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_zero_group" value="false" type="string" description="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="greedy_group_resolution" value="true" type="string" description="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities. Also adds the resolved ambiguity groups to output." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="no_cleanup" value="false" type="string" description="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="all_PSMs" value="false" type="string" description="Consider all PSMs of each peptide, instead of only the best one" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="group_level" value="false" type="string" description="Perform inference on protein group level (instead of individual protein level). This will lead to higher probabilities for (bigger) protein groups." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="accuracy" value="" type="string" description="Accuracy level of start parameters. There is a trade-off between accuracy and runtime. Empty uses the default ('best')." required="false" advanced="true" restrictions=",best,relaxed,sloppy" /> | |
| <ITEM name="log2_states" value="0" type="int" description="Binary logarithm of the max. number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="log2_states_precalc" value="0" type="int" description="Like 'log2_states', but allows to set a separate limit for the precalculation" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="prob" description="Probability values for running Fido directly, i.e. without parameter estimation (in which case other settings, except 'log2_states', are ignored)"> | |
| <ITEM name="protein" value="0" type="double" description="Protein prior probability ('gamma' parameter)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="peptide" value="0" type="double" description="Peptide emission probability ('alpha' parameter)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="spurious" value="0" type="double" description="Spurious peptide identification probability ('beta' parameter)" required="false" advanced="false" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FalseDiscoveryRate" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-230" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1270" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Identification input file containing a search against a concatenated sequence database. Either specify '-in' alone or 'in_target' together with 'in_decoy' as input." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="in_target" value="" type="input-file" description="Identification input file containing a search against a target-only database." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="in_decoy" value="" type="input-file" description="Identification input file containing a search against a decoy-only database." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Identification output with annotated FDR" required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="proteins_only" value="false" type="string" description="If set only the FDR on protein level is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="peptides_only" value="false" type="string" description="If set only the FDR on peptide (PSM) level is calculated" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameter section for the FDR calculation algorithm"> | |
| <ITEM name="no_qvalues" value="false" type="string" description="If 'true' strict FDRs will be calculated instead of q-values (the default)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="use_all_hits" value="false" type="string" description="If 'true' not only the first hit, but all are used (peptides only)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="split_charge_variants" value="false" type="string" description="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="treat_runs_separately" value="false" type="string" description="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="add_decoy_peptides" value="false" type="string" description="If 'true' decoy peptides will be written to output file, too. The q-value is set to the closest target score." required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-230" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1450" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="length" value=":" type="string" description="Keep only peptide hits with a sequence length in this range." required="false" advanced="false" /> | |
| <ITEM name="charge" value=":" type="string" description="Keep only peptide hits with charge states in this range." required="false" advanced="false" /> | |
| <ITEM name="var_mods" value="false" type="string" description="Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="unique" value="false" type="string" description="If a peptide hit occurs more than once per peptide ID, only one instance is kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="unique_per_protein" value="false" type="string" description="Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_protein_hits" value="false" type="string" description="Proteins not referenced by a peptide are retained in the IDs." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_decoys" value="false" type="string" description="Remove proteins according to the information in the user parameters. Usually used in combination with 'delete_unreferenced_peptide_hits'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="delete_unreferenced_peptide_hits" value="false" type="string" description="Peptides not referenced by any protein are deleted in the IDs. Usually used in combination with 'score:prot' or 'thresh:prot'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="precursor" description="Filtering by precursor RT or m/z"> | |
| <ITEM name="rt" value=":" type="string" description="Retention time range to extract." required="false" advanced="false" /> | |
| <ITEM name="mz" value=":" type="string" description="Mass-to-charge range to extract." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="score" description="Filtering by peptide/protein score."> | |
| <ITEM name="pep" value="0" type="double" description="The score which should be reached by a peptide hit to be kept." required="false" advanced="false" /> | |
| <ITEM name="prot" value="0" type="double" description="The score which should be reached by a protein hit to be kept. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="thresh" description="Filtering by significance threshold"> | |
| <ITEM name="pep" value="0" type="double" description="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." required="false" advanced="false" /> | |
| <ITEM name="prot" value="0" type="double" description="Keep a protein hit only if its score is above this fraction of the protein significance threshold. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="whitelist" description="Filtering by whitelisting (only peptides/proteins from a given set can pass)"> | |
| <ITEM name="proteins" value="" type="input-file" description="Filename of a FASTA file containing protein sequences.#br#All peptides that are not referencing a protein in this file are removed.#br#All proteins whose accessions are not present in this file are removed." required="false" advanced="false" supported_formats="*.fasta" /> | |
| <ITEMLIST name="protein_accessions" type="string" description="All peptides that do not reference at least one of the provided protein accession are removed.#br#Only proteins of the provided list are retained." required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="peptides" value="" type="input-file" description="Only peptides with the same sequence and modification assignment as any peptide in this file are kept. Use with 'whitelist:ignore_modifications' to only compare by sequence.#br#" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="ignore_modifications" value="false" type="string" description="Compare whitelisted peptides by sequence only." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="modifications" type="string" description="Keep only peptides with sequences that contain (any of) the selected modification(s)" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="blacklist" description="Filtering by blacklisting (only peptides/proteins NOT present in a given set can pass)"> | |
| <ITEM name="proteins" value="" type="input-file" description="Filename of a FASTA file containing protein sequences.#br#All peptides that are referencing a protein in this file are removed.#br#All proteins whose accessions are present in this file are removed." required="false" advanced="false" supported_formats="*.fasta" /> | |
| <ITEMLIST name="protein_accessions" type="string" description="All peptides that reference at least one of the provided protein accession are removed.#br#Only proteins not in the provided list are retained." required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="peptides" value="" type="input-file" description="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out. Use with 'blacklist:ignore_modifications' to only compare by sequence.#br#" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="ignore_modifications" value="false" type="string" description="Compare blacklisted peptides by sequence only." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="modifications" type="string" description="Remove all peptides with sequences that contain (any of) the selected modification(s)" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="rt" description="Filtering by RT predicted by 'RTPredict'"> | |
| <ITEM name="p_value" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict." required="false" advanced="true" restrictions="0:1" /> | |
| <ITEM name="p_value_1st_dim" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict for first dimension." required="false" advanced="true" restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="mz" description="Filtering by mass error"> | |
| <ITEM name="error" value="-1" type="double" description="Filtering by deviation to theoretical mass (disabled for negative values)." required="false" advanced="false" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Absolute or relative error." required="false" advanced="false" restrictions="Da,ppm" /> | |
| </NODE> | |
| <NODE name="best" description="Filtering best hits per spectrum (for peptides) or from proteins"> | |
| <ITEM name="n_peptide_hits" value="0" type="int" description="Keep only the 'n' highest scoring peptide hits per spectrum (for n > 0)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="n_protein_hits" value="0" type="int" description="Keep only the 'n' highest scoring protein hits (for n > 0)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="strict" value="false" type="string" description="Keep only the highest scoring peptide hit.#br#Similar to n_peptide_hits=1, but if there are ties between two or more highest scoring hits, none are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="n_to_m_peptide_hits" value=":" type="string" description="Peptide hit rank range to extracts" required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FeatureFinderMultiplex" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="470" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="30" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="LC-MS dataset in centroid or profile mode" required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="Set of all identified peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group." required="false" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="out_features" value="" type="output-file" description="Optional output file containing the individual peptide features in 'out'." required="false" advanced="true" supported_formats="*.featureXML" /> | |
| <ITEM name="out_mzq" value="" type="output-file" description="Optional output file of MzQuantML." required="false" advanced="true" supported_formats="*.mzq" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameters for the algorithm."> | |
| <ITEM name="labels" value="" type="string" description="Labels used for labelling the samples. [...] specifies the labels for a single sample. For example#br##br#[][Lys8,Arg10] ... SILAC#br#[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC#br#[Dimethyl0][Dimethyl6] ... Dimethyl#br#[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl#br#[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL" required="false" advanced="false" /> | |
| <ITEM name="charge" value="1:5" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." required="false" advanced="false" /> | |
| <ITEM name="isotopes_per_peptide" value="3:5" type="string" description="Range of isotopes per peptide in the sample. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " required="false" advanced="true" /> | |
| <ITEM name="rt_typical" value="50" type="double" description="Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="rt_min" value="10" type="double" description="Lower bound for the retention time [s]. (Any peptides seen for a shorter time period are not reported.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="30" type="double" description="m/z tolerance for search of peak patterns." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_unit" value="ppm" type="string" description="Unit of the 'mz_tolerance' parameter." required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="intensity_cutoff" value="10" type="double" description="Lower bound for the intensity of isotopic peaks." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="peptide_similarity" value="0.9" type="double" description="Two peptides in a multiplet are expected to have the same isotopic pattern. This parameter is a lower bound on their similarity." required="false" advanced="false" restrictions="-1:1" /> | |
| <ITEM name="averagine_similarity" value="0.8" type="double" description="The isotopic pattern of a peptide should resemble the averagine model at this m/z position. This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model." required="false" advanced="false" restrictions="-1:1" /> | |
| <ITEM name="averagine_similarity_scaling" value="0.75" type="double" description="Let x denote this scaling factor, and p the averagine similarity parameter. For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -> p' = p and x = 1 -> p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)" required="false" advanced="true" restrictions="0:1" /> | |
| <ITEM name="missed_cleavages" value="0" type="int" description="Maximum number of missed cleavages due to incomplete digestion. (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="knock_out" value="false" type="string" description="Is it likely that knock-outs are present? (Supported for doublex, triplex and quadruplex experiments only.)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="averagine_type" value="peptide" type="string" description="The type of averagine to use, currently RNA, DNA or peptide" required="false" advanced="true" restrictions="peptide,RNA,DNA" /> | |
| </NODE> | |
| <NODE name="labels" description="Isotopic labels that can be specified in section 'algorithm:labels'."> | |
| <ITEM name="Arg6" value="6.0201290268" type="double" description="Label:13C(6) | C(-6) 13C(6) | unimod #188" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Arg10" value="10.0082686" type="double" description="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys4" value="4.0251069836" type="double" description="Label:2H(4) | H(-4) 2H(4) | unimod #481" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys6" value="6.0201290268" type="double" description="Label:13C(6) | C(-6) 13C(6) | unimod #188" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys8" value="8.0141988132" type="double" description="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Leu3" value="3.01883" type="double" description="Label:2H(3) | H(-3) 2H(3) | unimod #262" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl0" value="28.0313" type="double" description="Dimethyl | H(4) C(2) | unimod #36" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl4" value="32.056407" type="double" description="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl6" value="34.063117" type="double" description="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl8" value="36.07567" type="double" description="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL0" value="105.021464" type="double" description="ICPL | H(3) C(6) N O | unimod #365" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL4" value="109.046571" type="double" description="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL6" value="111.041593" type="double" description="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL10" value="115.0667" type="double" description="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDMapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="470" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="690" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="id" value="" type="input-file" description="Protein/peptide identifications file" required="true" advanced="false" supported_formats="*.mzid,*.idXML" /> | |
| <ITEM name="in" value="" type="input-file" description="Feature map/consensus map file" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML,*.mzq" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file (the format depends on the input file format)." required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML,*.mzq" /> | |
| <ITEM name="rt_tolerance" value="5" type="double" description="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="20" type="double" description="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_measure" value="ppm" type="string" description="Unit of 'mz_tolerance'." required="false" advanced="false" restrictions="ppm,Da" /> | |
| <ITEM name="mz_reference" value="precursor" type="string" description="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" required="false" advanced="false" restrictions="precursor,peptide" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="feature" description="Additional options for featureXML input"> | |
| <ITEM name="use_centroid_rt" value="false" type="string" description="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="use_centroid_mz" value="false" type="string" description="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="consensus" description="Additional options for consensusXML input"> | |
| <ITEM name="use_subelements" value="false" type="string" description="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="annotate_ids_with_subelements" value="false" type="string" description="Store the map index of the sub-feature in the peptide ID." required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="150" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="690" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="length" value=":" type="string" description="Keep only peptide hits with a sequence length in this range." required="false" advanced="false" /> | |
| <ITEM name="charge" value=":" type="string" description="Keep only peptide hits with charge states in this range." required="false" advanced="false" /> | |
| <ITEM name="var_mods" value="false" type="string" description="Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="unique" value="false" type="string" description="If a peptide hit occurs more than once per peptide ID, only one instance is kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="unique_per_protein" value="false" type="string" description="Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="keep_unreferenced_protein_hits" value="false" type="string" description="Proteins not referenced by a peptide are retained in the IDs." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_decoys" value="false" type="string" description="Remove proteins according to the information in the user parameters. Usually used in combination with 'delete_unreferenced_peptide_hits'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="delete_unreferenced_peptide_hits" value="false" type="string" description="Peptides not referenced by any protein are deleted in the IDs. Usually used in combination with 'score:prot' or 'thresh:prot'." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="precursor" description="Filtering by precursor RT or m/z"> | |
| <ITEM name="rt" value=":" type="string" description="Retention time range to extract." required="false" advanced="false" /> | |
| <ITEM name="mz" value=":" type="string" description="Mass-to-charge range to extract." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="score" description="Filtering by peptide/protein score."> | |
| <ITEM name="pep" value="0.05" type="double" description="The score which should be reached by a peptide hit to be kept." required="false" advanced="false" /> | |
| <ITEM name="prot" value="0" type="double" description="The score which should be reached by a protein hit to be kept. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="thresh" description="Filtering by significance threshold"> | |
| <ITEM name="pep" value="0" type="double" description="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." required="false" advanced="false" /> | |
| <ITEM name="prot" value="0" type="double" description="Keep a protein hit only if its score is above this fraction of the protein significance threshold. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="whitelist" description="Filtering by whitelisting (only peptides/proteins from a given set can pass)"> | |
| <ITEM name="proteins" value="" type="input-file" description="Filename of a FASTA file containing protein sequences.#br#All peptides that are not referencing a protein in this file are removed.#br#All proteins whose accessions are not present in this file are removed." required="false" advanced="false" supported_formats="*.fasta" /> | |
| <ITEMLIST name="protein_accessions" type="string" description="All peptides that do not reference at least one of the provided protein accession are removed.#br#Only proteins of the provided list are retained." required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="peptides" value="" type="input-file" description="Only peptides with the same sequence and modification assignment as any peptide in this file are kept. Use with 'whitelist:ignore_modifications' to only compare by sequence.#br#" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="ignore_modifications" value="false" type="string" description="Compare whitelisted peptides by sequence only." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="modifications" type="string" description="Keep only peptides with sequences that contain (any of) the selected modification(s)" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="blacklist" description="Filtering by blacklisting (only peptides/proteins NOT present in a given set can pass)"> | |
| <ITEM name="proteins" value="" type="input-file" description="Filename of a FASTA file containing protein sequences.#br#All peptides that are referencing a protein in this file are removed.#br#All proteins whose accessions are present in this file are removed." required="false" advanced="false" supported_formats="*.fasta" /> | |
| <ITEMLIST name="protein_accessions" type="string" description="All peptides that reference at least one of the provided protein accession are removed.#br#Only proteins not in the provided list are retained." required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="peptides" value="" type="input-file" description="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out. Use with 'blacklist:ignore_modifications' to only compare by sequence.#br#" required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="ignore_modifications" value="false" type="string" description="Compare blacklisted peptides by sequence only." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="modifications" type="string" description="Remove all peptides with sequences that contain (any of) the selected modification(s)" required="false" advanced="false" restrictions="2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (D),ADP-Ribosyl (E),ADP-Ribosyl (K),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AHA-Alkyne (M),AHA-Alkyne-KDDDD (M),AHA-SS (M),AHA-SS_CAM (M),AMTzHexNAc2 (N),AMTzHexNAc2 (S),AMTzHexNAc2 (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3) (S),Acetyl:2H(3) (T),Acetyl:2H(3) (Y),Acetyldeoxyhypusine (K),Acetylhypusine (K),Ahx2+Hsl (C-term),Ala->Arg (A),Ala->Asn (A),Ala->Asp (A),Ala->Cys (A),Ala->Gln (A),Ala->Glu (A),Ala->Gly (A),Ala->His (A),Ala->Lys (A),Ala->Met (A),Ala->Phe (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Trp (A),Ala->Tyr (A),Ala->Val (A),Ala->Xle (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg (N-term),Arg->Ala (R),Arg->Asn (R),Arg->Asp (R),Arg->Cys (R),Arg->Gln (R),Arg->Glu (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Phe (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg->Tyr (R),Arg->Val (R),Arg->Xle (R),Arg-loss (C-term R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Ala (N),Asn->Arg (N),Asn->Asp (N),Asn->Cys (N),Asn->Gln (N),Asn->Glu (N),Asn->Gly (N),Asn->His (N),Asn->Lys (N),Asn->Met (N),Asn->Phe (N),Asn->Pro (N),Asn->Ser (N),Asn->Thr (N),Asn->Trp (N),Asn->Tyr (N),Asn->Val (N),Asn->Xle (N),Asp->Ala (D),Asp->Arg (D),Asp->Asn (D),Asp->Cys (D),Asp->Gln (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Lys (D),Asp->Met (D),Asp->Phe (D),Asp->Pro (D),Asp->Ser (D),Asp->Thr (D),Asp->Trp (D),Asp->Tyr (D),Asp->Val (D),Asp->Xle (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),BMP-piperidinol (C),BMP-piperidinol (M),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),Biotin:Cayman-10013 (C),Biotin:Cayman-10141 (C),Biotin:Invitrogen-M1602 (C),Biotin:Sigma-B1267 (C),Biotin:Thermo-21325 (K),Biotin:Thermo-21345 (Q),Biotin:Thermo-21360 (C-term),Biotin:Thermo-21901+2H2O (C),Biotin:Thermo-21901+H2O (C),Biotin:Thermo-21911 (C),Biotin:Thermo-33033 (N-term),Biotin:Thermo-33033-H (N-term),Biotin:Thermo-88310 (K),Biotin:Thermo-88317 (S),Biotin:Thermo-88317 (Y),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromo (Y),Bromobimane (C),Butyryl (K),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),Carbamidomethyl (S),Carbamidomethyl (T),Carbamidomethyl (Y),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (H),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDMAP (N-term),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),CoenzymeA (C),CresylSaligeninPhosphate (H),CresylSaligeninPhosphate (K),CresylSaligeninPhosphate (R),CresylSaligeninPhosphate (S),CresylSaligeninPhosphate (T),CresylSaligeninPhosphate (Y),Cresylphosphate (H),Cresylphosphate (K),Cresylphosphate (R),Cresylphosphate (S),Cresylphosphate (T),Cresylphosphate (Y),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),Crotonyl (K),CuSMo (C),Cy3-maleimide (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Ala (C),Cys->Arg (C),Cys->Asn (C),Cys->Asp (C),Cys->Dha (C),Cys->Gln (C),Cys->Glu (C),Cys->Gly (C),Cys->His (C),Cys->Lys (C),Cys->Met (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Pro (C),Cys->Ser (C),Cys->Thr (C),Cys->Trp (C),Cys->Tyr (C),Cys->Val (C),Cys->Xle (C),Cys->ethylaminoAla (C),Cys->methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DEDGFLYMVYASQETFG (K),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DMPO (C),DMPO (H),DMPO (Y),DNCB_hapten (C),DNCB_hapten (H),DNCB_hapten (K),DNCB_hapten (Y),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),Dap-DSP (A),Dap-DSP (E),Dap-DSP (K),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)N(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(2) (N-term),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2) (N-term),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(3)O(1) (C),Delta:H(6)C(3)O(1) (H),Delta:H(6)C(3)O(1) (K),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(1) (L),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Deoxyhypusine (K),Dethiomethyl (M),DiART6plex (K),DiART6plex (N-term),DiART6plex (Y),DiART6plex115 (K),DiART6plex115 (N-term),DiART6plex115 (Y),DiART6plex116/119 (K),DiART6plex116/119 (N-term),DiART6plex116/119 (Y),DiART6plex117 (K),DiART6plex117 (N-term),DiART6plex117 (Y),DiART6plex118 (K),DiART6plex118 (N-term),DiART6plex118 (Y),DiLeu4plex (K),DiLeu4plex (N-term),DiLeu4plex (Y),DiLeu4plex115 (K),DiLeu4plex115 (N-term),DiLeu4plex115 (Y),DiLeu4plex117 (K),DiLeu4plex117 (N-term),DiLeu4plex117 (Y),DiLeu4plex118 (K),DiLeu4plex118 (N-term),DiLeu4plex118 (Y),Diacylglycerol (C),Dibromo (Y),Dicarbamidomethyl (C),Dicarbamidomethyl (H),Dicarbamidomethyl (K),Dicarbamidomethyl (N-term),Dicarbamidomethyl (R),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Diethylphosphate (C),Diethylphosphate (H),Diethylphosphate (K),Diethylphosphate (N-term),Diethylphosphate (S),Diethylphosphate (T),Diethylphosphate (Y),Difuran (Y),Dihydroxyimidazolidine (R),Diiodo (H),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (N-term),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6) (K),Dimethyl:2H(6) (N-term),Dimethyl:2H(6) (R),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyridyl (C),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDEDTIDVFQQQTGG (K),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EEEDVIEVYQEQTGG (K),EGCG1 (C),EGCG2 (C),EHD-diphenylpentanone (C),EHD-diphenylpentanone (M),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),Ethyl+Deamidated (N),Ethyl+Deamidated (Q),Ethylphosphate (K),Ethylphosphate (N-term),Ethylphosphate (S),Ethylphosphate (T),Ethylphosphate (Y),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (A),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),Furan (Y),G-H1 (R),GG (C),GG (K),GG (S),GG (T),GGQ (K),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),Galactosyl (K),GeranylGeranyl (C),Gln->Ala (Q),Gln->Arg (Q),Gln->Asn (Q),Gln->Asp (Q),Gln->Cys (Q),Gln->Glu (Q),Gln->Gly (Q),Gln->His (Q),Gln->Lys (Q),Gln->Met (Q),Gln->Phe (Q),Gln->Pro (Q),Gln->Ser (Q),Gln->Thr (Q),Gln->Trp (Q),Gln->Tyr (Q),Gln->Val (Q),Gln->Xle (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Arg (E),Glu->Asn (E),Glu->Asp (E),Glu->Cys (E),Glu->Gln (E),Glu->Gly (E),Glu->His (E),Glu->Lys (E),Glu->Met (E),Glu->Phe (E),Glu->Pro (E),Glu->Ser (E),Glu->Thr (E),Glu->Trp (E),Glu->Tyr (E),Glu->Val (E),Glu->Xle (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Gluconoylation (K),Gluconoylation (N-term),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly (K),Gly (S),Gly (T),Gly->Ala (G),Gly->Arg (G),Gly->Asn (G),Gly->Asp (G),Gly->Cys (G),Gly->Gln (G),Gly->Glu (G),Gly->His (G),Gly->Lys (G),Gly->Met (G),Gly->Phe (G),Gly->Pro (G),Gly->Ser (G),Gly->Thr (G),Gly->Trp (G),Gly->Tyr (G),Gly->Val (G),Gly->Xle (G),Gly-loss+Amide (C-term G),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),Guanidinyl (N-term),HCysThiolactone (K),HCysteinyl (C),HMVK (C),HN2_mustard (C),HN2_mustard (H),HN2_mustard (K),HN3_mustard (C),HN3_mustard (H),HN3_mustard (K),HNE (A),HNE (C),HNE (H),HNE (K),HNE (L),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (S),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex(5)HexNAc(4)NeuAc(1) (N),Hex(5)HexNAc(4)NeuAc(2) (N),Hex1HexNAc1 (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His->Ala (H),His->Arg (H),His->Asn (H),His->Asp (H),His->Cys (H),His->Gln (H),His->Glu (H),His->Gly (H),His->Lys (H),His->Met (H),His->Phe (H),His->Pro (H),His->Ser (H),His->Thr (H),His->Trp (H),His->Tyr (H),His->Val (H),His->Xle (H),Homocysteic_acid (M),Hydroxamic_acid (D),Hydroxamic_acid (E),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICDID (C),ICDID:2H(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMEHex(2)NeuAc(1) (K),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Iodoacetanilide (C),Iodoacetanilide (K),Iodoacetanilide (N-term),Iodoacetanilide:13C(6) (C),Iodoacetanilide:13C(6) (K),Iodoacetanilide:13C(6) (N-term),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),LRGG (K),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(3) (A),Label:13C(3)15N(1) (A),Label:13C(4) (M),Label:13C(4)+Oxidation (M),Label:13C(4)15N(1) (D),Label:13C(4)15N(2)+GG (K),Label:13C(5) (P),Label:13C(5)15N(1) (E),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GG (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GG (K),Label:13C(6)15N(4) (R),Label:13C(6)15N(4)+Dimethyl (R),Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R),Label:13C(6)15N(4)+Methyl (R),Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(10) (L),Label:2H(3) (L),Label:2H(3) (M),Label:2H(3)+Oxidation (M),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GG (K),Label:2H(4)13C(1) (R),Label:2H(6)15N(1) (P),Label:2H(7)15N(4) (R),Label:2H(9)13C(6)15N(2) (K),Leu->MetOx (L),Lipoyl (K),Lys (N-term),Lys->Ala (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->Asp (K),Lys->CamCys (K),Lys->Cys (K),Lys->Gln (K),Lys->Glu (K),Lys->Gly (K),Lys->His (K),Lys->Met (K),Lys->MetOx (K),Lys->Phe (K),Lys->Pro (K),Lys->Ser (K),Lys->Thr (K),Lys->Trp (K),Lys->Tyr (K),Lys->Val (K),Lys->Xle (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MM-diphenylpentanone (C),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met->Aha (M),Met->Ala (M),Met->Arg (M),Met->Asn (M),Met->Asp (M),Met->Cys (M),Met->Gln (M),Met->Glu (M),Met->Gly (M),Met->His (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Lys (M),Met->Phe (M),Met->Pro (M),Met->Ser (M),Met->Thr (M),Met->Trp (M),Met->Tyr (M),Met->Val (M),Met->Xle (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3) (K),Methyl:2H(3) (R),Methyl:2H(3)+Acetyl:2H(3) (K),Methyl:2H(3)13C(1) (K),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (K),Methylthio (N),Methylthio (N-term),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),MurNAc (A),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),N-dimethylphosphate (S),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NEM:2H(5)+H2O (C),NEMsulfur (C),NEMsulfurWater (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NHS-fluorescein (K),NIC (K),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),NeuAc (N),NeuAc (S),NeuAc (T),NeuGc (N),NeuGc (S),NeuGc (T),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Et-N-diMePhospho (S),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (C),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),Oxidation+NEM (C),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PS_Hapten (C),PS_Hapten (H),PS_Hapten (K),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),Phe->Ala (F),Phe->Arg (F),Phe->Asn (F),Phe->Asp (F),Phe->CamCys (F),Phe->Cys (F),Phe->Gln (F),Phe->Glu (F),Phe->Gly (F),Phe->His (F),Phe->Lys (F),Phe->Met (F),Phe->Pro (F),Phe->Ser (F),Phe->Thr (F),Phe->Trp (F),Phe->Tyr (F),Phe->Val (F),Phe->Xle (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (K),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoHexNAc (T),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphogluconoylation (K),Phosphogluconoylation (N-term),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro->Ala (P),Pro->Arg (P),Pro->Asn (P),Pro->Asp (P),Pro->Cys (P),Pro->Gln (P),Pro->Glu (P),Pro->Gly (P),Pro->His (P),Pro->Lys (P),Pro->Met (P),Pro->Phe (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->Trp (P),Pro->Tyr (P),Pro->Val (P),Pro->Xle (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide (K),Propionamide (N-term),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl (T),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),Propiophenone (C),Propiophenone (H),Propiophenone (K),Propiophenone (R),Propiophenone (S),Propiophenone (T),Propiophenone (W),Propyl (K),Propyl (N-term),Propyl:2H(6) (K),Propyl:2H(6) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),PyridoxalPhosphateH2 (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),QTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Saligenin (H),Saligenin (K),SecCarbamidomethyl (C),SecNEM (C),SecNEM:2H(5) (C),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Asp (S),Ser->Cys (S),Ser->Gln (S),Ser->Glu (S),Ser->Gly (S),Ser->His (S),Ser->Lys (S),Ser->Met (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (S),Ser->Val (S),Ser->Xle (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfide (W),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),SulfurDioxide (C),TAMRA-FP (S),TAMRA-FP (Y),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (H),TMT (K),TMT (N-term),TMT (S),TMT (T),TMT2plex (H),TMT2plex (K),TMT2plex (N-term),TMT2plex (S),TMT2plex (T),TMT6plex (H),TMT6plex (K),TMT6plex (N-term),TMT6plex (S),TMT6plex (T),TNBS (K),TNBS (N-term),Thiadiazole (C),Thiazolidine (N-term C),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr->Ala (T),Thr->Arg (T),Thr->Asn (T),Thr->Asp (T),Thr->Cys (T),Thr->Gln (T),Thr->Glu (T),Thr->Gly (T),Thr->His (T),Thr->Lys (T),Thr->Met (T),Thr->Phe (T),Thr->Pro (T),Thr->Ser (T),Thr->Trp (T),Thr->Tyr (T),Thr->Val (T),Thr->Xle (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trimethyl:13C(3)2H(9) (K),Trimethyl:13C(3)2H(9) (R),Trimethyl:2H(9) (K),Trimethyl:2H(9) (R),Trioxidation (C),Trioxidation (W),Trioxidation (Y),Trp->Ala (W),Trp->Arg (W),Trp->Asn (W),Trp->Asp (W),Trp->Cys (W),Trp->Gln (W),Trp->Glu (W),Trp->Gly (W),Trp->His (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Lys (W),Trp->Met (W),Trp->Oxolactone (W),Trp->Phe (W),Trp->Pro (W),Trp->Ser (W),Trp->Thr (W),Trp->Tyr (W),Trp->Val (W),Trp->Xle (W),Tyr->Ala (Y),Tyr->Arg (Y),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->Gln (Y),Tyr->Glu (Y),Tyr->Gly (Y),Tyr->His (Y),Tyr->Lys (Y),Tyr->Met (Y),Tyr->Phe (Y),Tyr->Pro (Y),Tyr->Ser (Y),Tyr->Thr (Y),Tyr->Trp (Y),Tyr->Val (Y),Tyr->Xle (Y),Ub-Br2 (C),Ub-VME (C),Ub-amide (C),Ub-fluorescein (C),UgiJoullie (D),UgiJoullie (E),UgiJoullieProGly (D),UgiJoullieProGly (E),UgiJoullieProGlyProGly (D),UgiJoullieProGlyProGly (E),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Arg (V),Val->Asn (V),Val->Asp (V),Val->Cys (V),Val->Gln (V),Val->Glu (V),Val->Gly (V),Val->His (V),Val->Lys (V),Val->Met (V),Val->Phe (V),Val->Pro (V),Val->Ser (V),Val->Thr (V),Val->Trp (V),Val->Tyr (V),Val->Xle (V),Withaferin (C),Xle->Ala (I),Xle->Ala (L),Xle->Arg (I),Xle->Arg (L),Xle->Asn (I),Xle->Asn (L),Xle->Asp (I),Xle->Asp (L),Xle->Cys (I),Xle->Cys (L),Xle->Gln (I),Xle->Gln (L),Xle->Glu (I),Xle->Glu (L),Xle->Gly (I),Xle->Gly (L),Xle->His (I),Xle->His (L),Xle->Lys (I),Xle->Lys (L),Xle->Met (I),Xle->Met (L),Xle->Phe (I),Xle->Phe (L),Xle->Pro (I),Xle->Pro (L),Xle->Ser (I),Xle->Ser (L),Xle->Thr (I),Xle->Thr (L),Xle->Trp (I),Xle->Trp (L),Xle->Tyr (I),Xle->Tyr (L),Xle->Val (I),Xle->Val (L),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-de (K),Xlink:DMP-s (K),Xlink:DSS (K),Xlink:DST (K),Xlink:DTSSP (K),Xlink:EGS (K),Xlink:EGScleaved (K),Xlink:SMCC (C),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),azole (C),azole (S),benzylguanidine (K),biotinAcrolein298 (C),biotinAcrolein298 (H),biotinAcrolein298 (K),bisANS-sulfonates (K),bisANS-sulfonates (S),bisANS-sulfonates (T),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (N),dHex (S),dHex (T),dHex(1)Hex(1) (S),dHex(1)Hex(1) (T),dHex(1)Hex(2) (S),dHex(1)Hex(2) (T),dHex(1)Hex(3) (S),dHex(1)Hex(3) (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4) (S),dHex(1)Hex(4) (T),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5) (S),dHex(1)Hex(5) (T),dHex(1)Hex(5)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N),dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N),dHex(1)Hex(6) (S),dHex(1)Hex(6) (T),dNIC (K),dNIC (N-term),dichlorination (C),dichlorination (Y),ethylamino (S),ethylamino (T),ethylsulfonylethyl (C),ethylsulfonylethyl (H),ethylsulfonylethyl (K),glucosone (R),glycidamide (K),glycidamide (N-term),iTRAQ4plex (H),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (S),iTRAQ4plex (T),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (H),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (S),iTRAQ8plex (T),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),iodoTMT (C),iodoTMT (D),iodoTMT (E),iodoTMT (H),iodoTMT (K),iodoTMT6plex (C),iodoTMT6plex (D),iodoTMT6plex (E),iodoTMT6plex (H),iodoTMT6plex (K),lapachenole (C),mTRAQ (H),mTRAQ (K),mTRAQ (N-term),mTRAQ (S),mTRAQ (T),mTRAQ (Y),mTRAQ:13C(3)15N(1) (H),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (S),mTRAQ:13C(3)15N(1) (T),mTRAQ:13C(3)15N(1) (Y),mTRAQ:13C(6)15N(2) (H),mTRAQ:13C(6)15N(2) (K),mTRAQ:13C(6)15N(2) (N-term),mTRAQ:13C(6)15N(2) (S),mTRAQ:13C(6)15N(2) (T),mTRAQ:13C(6)15N(2) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),methylsulfonylethyl (C),methylsulfonylethyl (H),methylsulfonylethyl (K),phenylsulfonylethyl (C),phosphoRibosyl (D),phosphoRibosyl (E),phosphoRibosyl (R),probiotinhydrazide (P),pupylation (K),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="rt" description="Filtering by RT predicted by 'RTPredict'"> | |
| <ITEM name="p_value" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict." required="false" advanced="true" restrictions="0:1" /> | |
| <ITEM name="p_value_1st_dim" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict for first dimension." required="false" advanced="true" restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="mz" description="Filtering by mass error"> | |
| <ITEM name="error" value="-1" type="double" description="Filtering by deviation to theoretical mass (disabled for negative values)." required="false" advanced="false" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Absolute or relative error." required="false" advanced="false" restrictions="Da,ppm" /> | |
| </NODE> | |
| <NODE name="best" description="Filtering best hits per spectrum (for peptides) or from proteins"> | |
| <ITEM name="n_peptide_hits" value="0" type="int" description="Keep only the 'n' highest scoring peptide hits per spectrum (for n > 0)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="n_protein_hits" value="0" type="int" description="Keep only the 'n' highest scoring protein hits (for n > 0)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="strict" value="false" type="string" description="Keep only the highest scoring peptide hit.#br#Similar to n_peptide_hits=1, but if there are ties between two or more highest scoring hits, none are kept." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="n_to_m_peptide_hits" value=":" type="string" description="Peptide hit rank range to extracts" required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="14" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="770" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="690" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="Input file type -- default: determined from file extension or content" required="false" advanced="false" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="Output file type -- default: determined from file extension or content" required="false" advanced="false" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="rt" value=":" type="string" description="Retention time range to extract" required="false" advanced="false" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract (applies to ALL ms levels!)" required="false" advanced="false" /> | |
| <ITEM name="int" value="10000:1000000000000" type="string" description="Intensity range to extract" required="false" advanced="false" /> | |
| <ITEM name="sort" value="false" type="string" description="Sorts the output according to RT and m/z." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="peak_options" description="Peak data options"> | |
| <ITEM name="sn" value="0" type="double" description="Write peaks with S/N > 'sn' values only" required="false" advanced="false" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="pc_mz_range" value=":" type="string" description="MSn (n>=2) precursor filtering according to their m/z value. Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag." required="false" advanced="false" /> | |
| <ITEMLIST name="pc_mz_list" type="double" description="List of m/z values. If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept." required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract" required="false" advanced="false"> | |
| <LISTITEM value="1"/> | |
| <LISTITEM value="2"/> | |
| <LISTITEM value="3"/> | |
| </ITEMLIST> | |
| <ITEM name="sort_peaks" value="false" type="string" description="Sorts the peaks according to m/z" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="mz_precision" value="64" type="string" description="Store base64 encoded m/z data using 32 or 64 bit precision" required="false" advanced="false" restrictions="32,64" /> | |
| <ITEM name="int_precision" value="32" type="string" description="Store base64 encoded intensity data using 32 or 64 bit precision" required="false" advanced="false" restrictions="32,64" /> | |
| <ITEM name="indexed_file" value="false" type="string" description="Whether to add an index to the file when writing" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="numpress" description="Numpress compression for peak data"> | |
| <ITEM name="masstime" value="none" type="string" description="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" required="false" advanced="false" restrictions="none,linear,pic,slof" /> | |
| <ITEM name="masstime_error" value="0.0001" type="double" description="Maximal allowable error in m/z or rt dimension (set to 0.5 for pic)" required="false" advanced="false" /> | |
| <ITEM name="intensity" value="none" type="string" description="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" required="false" advanced="false" restrictions="none,linear,pic,slof" /> | |
| <ITEM name="intensity_error" value="0.0001" type="double" description="Maximal allowable error in intensity dimension (set to 0.5 for pic)" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="spectra" description="Remove spectra or select spectra (removing all others) with certain properties"> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode" required="false" advanced="false" restrictions="Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="remove_activation" value="" type="string" description="Remove MSn scans where any of its precursors features a certain activation method" required="false" advanced="false" restrictions="Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation" /> | |
| <ITEM name="remove_collision_energy" value=":" type="string" description="Remove MSn scans with a collision energy in the given interval" required="false" advanced="false" /> | |
| <ITEM name="remove_isolation_window_width" value=":" type="string" description="Remove MSn scans whose isolation window width is in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" required="false" advanced="false" restrictions="Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Retain MSn scans where any of its precursors features a certain activation method" required="false" advanced="false" restrictions="Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation" /> | |
| <ITEM name="select_collision_energy" value=":" type="string" description="Select MSn scans with a collision energy in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_isolation_window_width" value=":" type="string" description="Select MSn scans whose isolation window width is in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_polarity" value="" type="string" description="Retain MSn scans with a certain scan polarity" required="false" advanced="false" restrictions="unknown,positive,negative" /> | |
| </NODE> | |
| <NODE name="feature" description="Feature data options"> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="consensus" description="Consensus feature data options"> | |
| <ITEMLIST name="map" type="int" description="Maps to be extracted from a consensus" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="blackorwhitelist" description="Black or white listing of of MS2 spectra by consensus features"> | |
| <ITEM name="blacklist" value="true" type="string" description="True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept" required="false" advanced="false" restrictions="false,true" /> | |
| <ITEM name="file" value="" type="input-file" description="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.#br#If consensus:blackorwhitelist:maps is specified, only these will be used.#br#" required="false" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEMLIST name="maps" type="int" description="Maps used for black/white list filtering" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="rt" value="60" type="double" description="Retention tolerance [s] for precursor to consensus feature position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz" value="0.01" type="double" description="m/z tolerance [Th] for precursor to consensus feature position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="use_ppm_tolerance" value="false" type="string" description="If ppm tolerance should be used. Otherwise Da are used." required="false" advanced="false" restrictions="false,true" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="f_and_c" description="Feature & Consensus data options"> | |
| <ITEM name="charge" value=":" type="string" description="Charge range to extract" required="false" advanced="false" /> | |
| <ITEM name="size" value=":" type="string" description="Size range to extract" required="false" advanced="false" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple (=3 entries in the list), i.e. <name> 'lt|eq|gt' <value>; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!" required="false" advanced="false"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="id" description="ID options. The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="Remove features with id clashes (different sequences mapped to one feature)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="keep_best_score_id" value="false" type="string" description="in case of multiple peptide identifications, keep only the id with best score" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="Remove features with annotations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="false" type="string" description="Remove features without annotations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="false" type="string" description="Remove unassigned peptide identifications" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="blacklist" value="" type="input-file" description="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'id:rt' and 'id:mz' options.#br#This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="rt" value="0.1" type="double" description="Retention tolerance [s] for precursor to id position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz" value="0.001" type="double" description="m/z tolerance [Th] for precursor to id position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="blacklist_imperfect" value="false" type="string" description="Allow for mismatching precursor positions (see 'id:blacklist')" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="algorithm" description="S/N algorithm section"> | |
| <NODE name="SignalToNoise" description=""> | |
| <ITEM name="max_intensity" value="-1" type="int" description="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N." required="false" advanced="true" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="double" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" required="false" advanced="true" restrictions="0:999" /> | |
| <ITEM name="auto_max_percentile" value="95" type="int" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" required="false" advanced="true" restrictions="0:100" /> | |
| <ITEM name="auto_mode" value="0" type="int" description="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" required="false" advanced="true" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="double" description="window length in Thomson" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" required="false" advanced="false" restrictions="3:" /> | |
| <ITEM name="min_required_elements" value="10" type="int" description="minimum number of elements required in a window (otherwise it is considered sparse)" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="double" description="noise value used for sparse windows" required="false" advanced="true" /> | |
| <ITEM name="write_log_messages" value="true" type="string" description="Write out log messages in case of sparse windows or median in rightmost histogram bin" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="15" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="770" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="850" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="16" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="MapAlignerPoseClustering" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="770" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1010" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="input-file" description="Input files to align (all must have the same file type)" required="true" advanced="false" supported_formats="*.mzML,*.featureXML"> | |
| </ITEMLIST> | |
| <ITEMLIST name="out" type="output-file" description="Output files (same file type as 'in'). Either this option or 'trafo_out' has to be provided; they can be used together." required="false" advanced="false" supported_formats="*.mzML,*.featureXML"> | |
| </ITEMLIST> | |
| <ITEMLIST name="trafo_out" type="output-file" description="Transformation output files. Either this option or 'out' has to be provided; they can be used together." required="false" advanced="false" supported_formats="*.trafoXML"> | |
| </ITEMLIST> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="reference" description="Options to define a reference file (use either 'file' or 'index', not both)"> | |
| <ITEM name="file" value="" type="input-file" description="File to use as reference (same file format as input files required)" required="false" advanced="false" supported_formats="*.mzML,*.featureXML" /> | |
| <ITEM name="index" value="0" type="int" description="Use one of the input files as reference ('1' for the first file, etc.).#br#If '0', no explicit reference is set - the algorithm will select a reference." required="false" advanced="false" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="max_num_peaks_considered" value="1000" type="int" description="The maximal number of peaks/features to be considered per map. To use all, set to '-1'." required="false" advanced="false" restrictions="-1:" /> | |
| <NODE name="superimposer" description=""> | |
| <ITEM name="mz_pair_max_distance" value="0.5" type="double" description="Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="rt_pair_distance_fraction" value="0.1" type="double" description="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). " required="false" advanced="true" restrictions="0:1" /> | |
| <ITEM name="num_used_points" value="2000" type="int" description="Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1." required="false" advanced="false" restrictions="-1:" /> | |
| <ITEM name="scaling_bucket_size" value="0.005" type="double" description="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="shift_bucket_size" value="3" type="double" description="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="max_shift" value="1000" type="double" description="Maximal shift which is considered during histogramming (in seconds). This applies for both directions." required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="max_scaling" value="2" type="double" description="Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this." required="false" advanced="true" restrictions="1:" /> | |
| <ITEM name="dump_buckets" value="" type="string" description="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically." required="false" advanced="true" /> | |
| <ITEM name="dump_pairs" value="" type="string" description="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically." required="false" advanced="true" /> | |
| </NODE> | |
| <NODE name="pairfinder" description=""> | |
| <ITEM name="second_nearest_gap" value="2" type="double" description="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself." required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="use_identifications" value="false" type="string" description="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="100" type="double" description="Never pair features with a larger RT distance (in seconds)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="double" description="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="double" description="Final RT distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="5" type="double" description="Never pair features with larger m/z distance (unit defined by 'unit')" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Unit of the 'max_difference' parameter" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="double" description="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="double" description="Final m/z distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)"> | |
| <ITEM name="exponent" value="1" type="double" description="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="double" description="Final intensity distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="17" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="splitter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="590" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1010" type="double" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="18" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="MapRTTransformer" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="390" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1010" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file to transform (separated by blanks)" required="false" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file (same file type as 'in'). Either this option or 'trafo_out' has to be provided; they can be used together." required="false" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.idXML" /> | |
| <ITEM name="trafo_in" value="" type="input-file" description="Transformation to apply" required="true" advanced="false" supported_formats="*.trafoXML" /> | |
| <ITEM name="trafo_out" value="" type="output-file" description="Transformation output file. Either this option or 'out' has to be provided; they can be used together." required="false" advanced="false" supported_formats="*.trafoXML" /> | |
| <ITEM name="invert" value="false" type="string" description="Invert transformation (approximatively) before applying it" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="store_original_rt" value="false" type="string" description="Store the original retention times (before transformation) as meta data in the output file" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="model" description="Options to control the modeling of retention time transformations from data"> | |
| <ITEM name="type" value="none" type="string" description="Type of model" required="false" advanced="false" restrictions="none,linear,b_spline,lowess,interpolated" /> | |
| <NODE name="linear" description="Parameters for 'linear' model"> | |
| <ITEM name="symmetric_regression" value="false" type="string" description="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="b_spline" description="Parameters for 'b_spline' model"> | |
| <ITEM name="wavelength" value="0" type="double" description="Determines the amount of smoothing by setting the number of nodes for the B-spline. The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="num_nodes" value="5" type="int" description="Number of nodes for B-spline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="extrapolate" value="linear" type="string" description="Method to use for extrapolation beyond the original data range. 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)." required="false" advanced="false" restrictions="linear,b_spline,constant,global_linear" /> | |
| <ITEM name="boundary_condition" value="2" type="int" description="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" required="false" advanced="false" restrictions="0:2" /> | |
| </NODE> | |
| <NODE name="lowess" description="Parameters for 'lowess' model"> | |
| <ITEM name="span" value="0.666666666666667" type="double" description="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit." required="false" advanced="false" restrictions="0:1" /> | |
| <ITEM name="num_iterations" value="3" type="int" description="Number of robustifying iterations for lowess fitting." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="delta" value="-1" type="double" description="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this." required="false" advanced="false" /> | |
| <ITEM name="interpolation_type" value="cspline" type="string" description="Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation" required="false" advanced="false" restrictions="linear,cspline,akima" /> | |
| <ITEM name="extrapolation_type" value="four-point-linear" type="string" description="Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation." required="false" advanced="false" restrictions="two-point-linear,four-point-linear,global-linear" /> | |
| </NODE> | |
| <NODE name="interpolated" description="Parameters for 'interpolated' model"> | |
| <ITEM name="interpolation_type" value="cspline" type="string" description="Type of interpolation to apply." required="false" advanced="false" restrictions="linear,cspline,akima" /> | |
| <ITEM name="extrapolation_type" value="two-point-linear" type="string" description="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model. Note that global-linear may not be continuous at the border." required="false" advanced="false" restrictions="two-point-linear,four-point-linear,global-linear" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="19" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="390" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1250" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="20" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FeatureLinkerUnlabeledQT" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="390" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1650" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="input-file" description="input files separated by blanks" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="keep_subelements" value="false" type="string" description="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="use_identifications" value="false" type="string" description="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="nr_partitions" value="1" type="int" description="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="100" type="double" description="Never pair features with a larger RT distance (in seconds)." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="double" description="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="double" description="Final RT distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="5" type="double" description="Never pair features with larger m/z distance (unit defined by 'unit')" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Unit of the 'max_difference' parameter" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="double" description="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="double" description="Final m/z distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)"> | |
| <ITEM name="exponent" value="1" type="double" description="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="double" description="Final intensity distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="21" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="IDConflictResolver" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="210" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1650" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file (data annotated with identifications)" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file (data with one peptide identification per feature)" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="22" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="ConsensusMapNormalizer" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="10" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1650" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input file" required="true" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="algorithm_type" value="median" type="string" description="The normalization algorithm that is applied. 'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)" required="false" advanced="false" restrictions="robust_regression,median,median_shift,quantile" /> | |
| <ITEM name="ratio_threshold" value="0.67" type="double" description="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers." required="false" advanced="false" restrictions="0.001:1" /> | |
| <ITEM name="accession_filter" value="" type="string" description="Use only features with accessions (partially) matching this regular expression for computing the normalization factors. Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used." required="false" advanced="true" /> | |
| <ITEM name="description_filter" value="" type="string" description="Use only features with description (partially) matching this regular expression for computing the normalization factors. Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used." required="false" advanced="true" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="23" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="ProteinQuantifier" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-230" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="1650" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML,*.idXML" /> | |
| <ITEM name="protein_groups" value="" type="input-file" description="Protein inference results for the identification runs that were used to annotate the input (e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).#br#Information about indistinguishable proteins will be used for protein quantification." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file for protein abundances" required="false" advanced="false" supported_formats="*.csv" /> | |
| <ITEM name="peptide_out" value="" type="output-file" description="Output file for peptide abundances" required="false" advanced="false" supported_formats="*.csv" /> | |
| <ITEM name="top" value="0" type="int" description="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="average" value="sum" type="string" description="Averaging method used to compute protein abundances from peptide abundances" required="false" advanced="false" restrictions="median,mean,weighted_mean,sum" /> | |
| <ITEM name="include_all" value="false" type="string" description="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="filter_charge" value="false" type="string" description="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="ratios" value="false" type="string" description="Add the log2 ratios of the abundance values to the output. Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) ..." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="ratiosSILAC" value="false" type="string" description="Add the log2 ratios for a triple SILAC experiment to the output. Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="consensus" description="Additional options for consensus maps (and identification results comprising multiple runs)"> | |
| <ITEM name="normalize" value="false" type="string" description="Scale peptide abundances so that medians of all samples are equal" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="fix_peptides" value="false" type="string" description="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="format" description="Output formatting options"> | |
| <ITEM name="separator" value="," type="string" description="Character(s) used to separate fields; by default, the 'tab' character is used" required="false" advanced="false" /> | |
| <ITEM name="quoting" value="double" type="string" description="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" required="false" advanced="false" restrictions="none,double,escape" /> | |
| <ITEM name="replacement" value="_" type="string" description="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="edges" description=""> | |
| <NODE name="0" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/2" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/11" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
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| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/2" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="database" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/3" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="fasta" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <NODE name="source/target" description=""> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="source/target" description=""> | |
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| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="id" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
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| </NODE> | |
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| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| </NODE> | |
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| <NODE name="source/target" description=""> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
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| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="protein_groups" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="26" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="23/24" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="27" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="11/13" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </PARAMETERS> |
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