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| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">SILAC analysis pipeline for Thermo Orbi XL data with Mascot identification</p> | |
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| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">input [1]: mzML</p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">input [3]: fasta database</p> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">output [10]: protein abundances</p> | |
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| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">SILAC peptide pairs are detected in [4]. Sequences are identified in [2, 5-7].</p> | |
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| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Lars Nilse l.nilse@dunelm.org.uk</p> | |
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| <ITEMLIST name="file_names" type="string" description=""> | |
| <LISTITEM value="20120327_benchmark/yeast/Bert_20080625_BJS_yeast_1-1_01.mzML"/> | |
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| <NODE name="1" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="MascotAdapterOnline" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="20" type="float" description="" /> | |
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| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file in mzML format.#br#" tags="input file,required" restrictions="*.mzML" /> | |
| <ITEM name="out" value="" type="string" description="output file in IdXML format.#br#" tags="output file,required" restrictions="*.idXML" /> | |
| <ITEM name="keep_protein_links" value="false" type="string" description="The Mascot response file usually returns incomplete/wrong protein hits, so re-indexing the peptide hits is required. To avoid confusion why there are so few protein hits and force re-indexing, no proteins should be reported. To see the original (wrong) list, enable this flag." tags="advanced" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="Mascot_parameters" description="Mascot parameters used for searching"> | |
| <ITEM name="database" value="DEC_Yeast_orf060512" type="string" description="Name of the sequence database" /> | |
| <ITEM name="search_type" value="MIS" type="string" description="Name of the search type for the query" tags="advanced" restrictions="MIS,SQ,PMF" /> | |
| <ITEM name="enzyme" value="Trypsin" type="string" description="Name of enzyme used for the digestion" /> | |
| <ITEM name="instrument" value="Default" type="string" description="Instrument definition which specifies the fragmentation rules" /> | |
| <ITEM name="missed_cleavages" value="1" type="int" description="Number of missed cleavages allowed for the enzyme" restrictions="0:" /> | |
| <ITEM name="precursor_mass_tolerance" value="10" type="float" description="Tolerance of the precursor peaks" restrictions="0:" /> | |
| <ITEM name="precursor_error_units" value="ppm" type="string" description="Units of the precursor mass tolerance" restrictions="%,ppm,mmu,Da" /> | |
| <ITEM name="fragment_mass_tolerance" value="0.02" type="float" description="Tolerance of the peaks in the fragment spectrum" restrictions="0:" /> | |
| <ITEM name="fragment_error_units" value="Da" type="string" description="Units of the fragment peaks tolerance" restrictions="mmu,Da" /> | |
| <ITEM name="charges" value="1,2,3" type="string" description="Allowed charge states, given as a comma separated list of integers" /> | |
| <ITEM name="taxonomy" value="All entries" type="string" description="Taxonomy specification of the sequences" /> | |
| <ITEMLIST name="fixed_modifications" type="string" description="List of fixed modifications, according to UniMod definitions." restrictions="15dB-biotin (C),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),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 (E),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),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Ala->Asp (A),Ala->Glu (A),Ala->Gly (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Val (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->Cys (R),Arg->Gln (R),Arg->GluSA (R),Arg->Gly 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(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(3) (L),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GlyGly (K),Label:2H(9)13C(6)15N(2) (K),Leu->Arg (L),Leu->Gln (L),Leu->His (L),Leu->Met (L),Leu->MetOx (L),Leu->Phe (L),Leu->Pro (L),Leu->Ser (L),Leu->Trp (L),Leu->Val (L),LeuArgGlyGly (K),Lipoyl (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->CamCys (K),Lys->Gln (K),Lys->Glu (K),Lys->Ile (K),Lys->Met (K),Lys->MetOx (K),Lys->Thr (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),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->Arg (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Ile (M),Met->Leu (M),Met->Lys (M),Met->Thr (M),Met->Val (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)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (N),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),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),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),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),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Diethylphosphate (C),O-Diethylphosphate (H),O-Diethylphosphate (K),O-Diethylphosphate (S),O-Diethylphosphate (T),O-Diethylphosphate (Y),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Ethylphosphate (S),O-Ethylphosphate (T),O-Ethylphosphate (Y),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 (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),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PGA1-biotin (C),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),PentylamineBiotin (Q),Phe->CamCys (F),Phe->Cys (F),Phe->Ile (F),Phe->Ser (F),Phe->Tyr (F),Phe->Val (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),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->Gln (P),Pro->His (P),Pro->Leu (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (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),Quinone (W),Quinone (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),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Cys (S),Ser->Gly (S),Ser->Ile (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (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),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (K),TMT (N-term),TMT2plex (K),TMT2plex (N-term),TMT6plex (K),TMT6plex (N-term),TNBS (K),TNBS (N-term),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->Ile (T),Thr->Lys (T),Thr->Met (T),Thr->Pro (T),Thr->Ser (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trioxidation (C),Trp->Arg (W),Trp->Cys (W),Trp->Gly (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Leu (W),Trp->Oxolactone (W),Trp->Ser (W),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->His (Y),Tyr->Phe (Y),Tyr->Ser (Y),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Asp (V),Val->Glu (V),Val->Gly (V),Val->Ile (V),Val->Met (V),Val->Phe (V),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-s (K),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (S),dHex (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4) (N),dNIC (N-term),dichlorination (Y),ethylamino (S),ethylamino (T),glucosone (R),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),lapachenole (C),mTRAQ (K),mTRAQ (N-term),mTRAQ (Y),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),probiotinhydrazide (P),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| <LISTITEM value="Carbamidomethyl (C)"/> | |
| </ITEMLIST> | |
| <ITEMLIST name="variable_modifications" type="string" description="Variable modifications given as UniMod definitions." restrictions="15dB-biotin (C),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),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 (E),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),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Ala->Asp (A),Ala->Glu (A),Ala->Gly (A),Ala->Pro (A),Ala->Ser (A),Ala->Thr (A),Ala->Val (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->Cys (R),Arg->Gln (R),Arg->GluSA (R),Arg->Gly (R),Arg->His (R),Arg->Ile (R),Arg->Lys (R),Arg->Met (R),Arg->Npo (R),Arg->Orn (R),Arg->Pro (R),Arg->Ser (R),Arg->Thr (R),Arg->Trp (R),Arg2PG (R),Argbiotinhydrazide (R),Asn->Asp (N),Asn->His (N),Asn->Ile (N),Asn->Lys (N),Asn->Ser (N),Asn->Thr (N),Asn->Tyr (N),Asp->Ala (D),Asp->Asn (D),Asp->Glu (D),Asp->Gly (D),Asp->His (D),Asp->Tyr (D),Asp->Val (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),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-PEO4-hydrazide (C-term),Biotin-maleimide (C),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromobimane (C),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_1 (K),CLIP_TRAQ_1 (N-term),CLIP_TRAQ_1 (Y),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),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 (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),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),ChromoBiotin (K),CoenzymeA (C),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),CuSMo (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys->Arg (C),Cys->Dha (C),Cys->Gly (C),Cys->Oxoalanine (C),Cys->Phe (C),Cys->Ser (C),Cys->Trp (C),Cys->Tyr (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),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),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),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)O(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),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)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(6)O(1) (K),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),Dethiomethyl (M),Diacylglycerol (C),Dibromo (Y),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Dihydroxyimidazolidine (R),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),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)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),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),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-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),EthylAmide (N),EthylAmide (Q),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 (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),G-H1 (R),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),GalNAzBiotin (N),GalNAzBiotin (S),GalNAzBiotin (T),Galactosyl (K),GeranylGeranyl (C),Gln->Arg (Q),Gln->Glu (Q),Gln->His (Q),Gln->Leu (Q),Gln->Lys (Q),Gln->Pro (Q),Gln->pyro-Glu (N-term Q),Glu (E),Glu->Ala (E),Glu->Asp (E),Glu->Gln (E),Glu->Gly (E),Glu->Lys (E),Glu->Val (E),Glu->pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly->Ala (G),Gly->Arg (G),Gly->Asp (G),Gly->Cys (G),Gly->Glu (G),Gly->Ser (G),Gly->Trp (G),Gly->Val (G),Gly-loss+Amide (C-term G),GlyGly (C),GlyGly (K),GlyGly (S),GlyGly (T),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),HMVK (C),HNE (C),HNE (H),HNE (K),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 (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),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->Arg (H),His->Asn (H),His->Asp (H),His->Gln (H),His->Leu (H),His->Pro (H),His->Tyr (H),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),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),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Ile->Arg (I),Ile->Asn (I),Ile->Lys (I),Ile->Met (I),Ile->Phe (I),Ile->Ser (I),Ile->Thr (I),Ile->Val (I),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),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),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(4)15N(2)+GlyGly (K),Label:13C(5) (P),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)+GlyGly (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)+GlyGly (K),Label:13C(6)15N(4) (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(3) (L),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GlyGly (K),Label:2H(9)13C(6)15N(2) (K),Leu->Arg (L),Leu->Gln (L),Leu->His (L),Leu->Met (L),Leu->MetOx (L),Leu->Phe (L),Leu->Pro (L),Leu->Ser (L),Leu->Trp (L),Leu->Val (L),LeuArgGlyGly (K),Lipoyl (K),Lys->Allysine (K),Lys->AminoadipicAcid (K),Lys->Arg (K),Lys->Asn (K),Lys->CamCys (K),Lys->Gln (K),Lys->Glu (K),Lys->Ile (K),Lys->Met (K),Lys->MetOx (K),Lys->Thr (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),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->Arg (M),Met->Hpg (M),Met->Hse (C-term M),Met->Hsl (C-term M),Met->Ile (M),Met->Leu (M),Met->Lys (M),Met->Thr (M),Met->Val (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)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (N),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),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),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),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),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Diethylphosphate (C),O-Diethylphosphate (H),O-Diethylphosphate (K),O-Diethylphosphate (S),O-Diethylphosphate (T),O-Diethylphosphate (Y),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Ethylphosphate (S),O-Ethylphosphate (T),O-Ethylphosphate (Y),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 (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),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PGA1-biotin (C),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),PentylamineBiotin (Q),Phe->CamCys (F),Phe->Cys (F),Phe->Ile (F),Phe->Ser (F),Phe->Tyr (F),Phe->Val (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),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->Gln (P),Pro->His (P),Pro->Leu (P),Pro->Pyrrolidinone (P),Pro->Pyrrolidone (P),Pro->Ser (P),Pro->Thr (P),Pro->pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (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),Quinone (W),Quinone (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),Ser->Ala (S),Ser->Arg (S),Ser->Asn (S),Ser->Cys (S),Ser->Gly (S),Ser->Ile (S),Ser->Phe (S),Ser->Pro (S),Ser->Thr (S),Ser->Trp (S),Ser->Tyr (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),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (K),TMT (N-term),TMT2plex (K),TMT2plex (N-term),TMT6plex (K),TMT6plex (N-term),TNBS (K),TNBS (N-term),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->Ile (T),Thr->Lys (T),Thr->Met (T),Thr->Pro (T),Thr->Ser (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trioxidation (C),Trp->Arg (W),Trp->Cys (W),Trp->Gly (W),Trp->Hydroxykynurenin (W),Trp->Kynurenin (W),Trp->Leu (W),Trp->Oxolactone (W),Trp->Ser (W),Tyr->Asn (Y),Tyr->Asp (Y),Tyr->Cys (Y),Tyr->Dha (Y),Tyr->His (Y),Tyr->Phe (Y),Tyr->Ser (Y),VFQQQTGG (K),VIEVYQEQTGG (K),Val->Ala (V),Val->Asp (V),Val->Glu (V),Val->Gly (V),Val->Ile (V),Val->Met (V),Val->Phe (V),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-s (K),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (S),dHex (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4) (N),dNIC (N-term),dichlorination (Y),ethylamino (S),ethylamino (T),glucosone (R),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),lapachenole (C),mTRAQ (K),mTRAQ (N-term),mTRAQ (Y),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),probiotinhydrazide (P),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)"> | |
| <LISTITEM value="Acetyl (N-term)"/> | |
| <LISTITEM value="Oxidation (M)"/> | |
| </ITEMLIST> | |
| <ITEM name="mass_type" value="monoisotopic" type="string" description="Defines the mass type, either monoisotopic or average" restrictions="monoisotopic,average" /> | |
| <ITEM name="number_of_hits" value="10" type="int" description="Number of hits which should be returned, if 0 AUTO mode is enabled." restrictions="0:" /> | |
| <ITEM name="skip_spectrum_charges" value="false" type="string" description="Sometimes precursor charges are given for each spectrum but are wrong, setting this to 'true' does not write any charge information to the spectrum, the general charge information is however kept." restrictions="true,false" /> | |
| <ITEM name="search_title" value="OpenMS_search" type="string" description="Sets the title of the search." tags="advanced" /> | |
| <ITEM name="username" value="OpenMS" type="string" description="Sets the username which is mentioned in the results file." tags="advanced" /> | |
| <ITEM name="format" value="Mascot generic" type="string" description="Sets the format type of the peak list, this should not be changed." tags="advanced" /> | |
| <ITEM name="form_version" value="1.01" type="string" description="Sets the version of the peak list format, this should not be changed." tags="advanced" /> | |
| <ITEM name="peaklists_only" value="false" type="string" description="Skip the parameter header and the MIME parts; just write the peak lists" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq" type="string" description="MIME boundary" tags="advanced" /> | |
| </NODE> | |
| <NODE name="Mascot_server" description="Mascot server details"> | |
| <ITEM name="hostname" value="selbachsrv" type="string" description="Address of the host where Mascot listens, e.g. 'mascot-server' or '127.0.0.1'" /> | |
| <ITEM name="host_port" value="80" type="int" description="Port where the Mascot server listens, 80 should be a good guess" restrictions="0:" /> | |
| <ITEM name="server_path" value="mascot" type="string" description="Path on the server where Mascot server listens, 'mascot' should be a good guess" /> | |
| <ITEM name="timeout" value="1500" type="int" description="Timeout in seconds, after which the query is declared as failed.This is NOT the whole time the search takes, but the time in between two progress steps. Some Mascot servers freeze during this (unstable network etc) and idle forever, the connection is killed. Set this to 0 to disable timeout!" restrictions="0:" /> | |
| <ITEM name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq" type="string" description="Boundary for the MIME section" tags="advanced" /> | |
| <ITEM name="use_proxy" value="false" type="string" description="Flag which enabled the proxy usage for the http requests, please specify at least 'proxy_host' and 'proxy_port'" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="proxy_host" value="" type="string" description="Host where the proxy server runs on" tags="advanced" /> | |
| <ITEM name="proxy_port" value="0" type="int" description="Port where the proxy server listens" tags="advanced" restrictions="0:" /> | |
| <ITEM name="proxy_username" value="" type="string" description="Login name for the proxy server, if needed" tags="advanced" /> | |
| <ITEM name="proxy_password" value="" type="string" description="Login password for the proxy server, if needed" tags="advanced" /> | |
| <ITEM name="login" value="false" type="string" description="Flag which should be set 'true' if Mascot security is enabled; also set 'username' and 'password' then." restrictions="true,false" /> | |
| <ITEM name="username" value="" type="string" description="Name of the user if login is used (Mascot security must be enabled!)" /> | |
| <ITEM name="password" value="" type="string" description="Password of the user if login is used (Mascot security must be enabled!)" /> | |
| <ITEM name="query_master" value="false" type="string" description="If this option is set to true, query peptides will be returned with non-truncated lists, however, protein references of peptides will not be correct." tags="advanced" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="PeptideIndexer" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="20" type="float" description="" /> | |
| <ITEM name="y_pos" value="-400" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Input idXML file containing the identifications." tags="input file,required" restrictions="*.IdXML" /> | |
| <ITEM name="fasta" value="" type="string" description="Input sequence database in FASTA format. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'" tags="input file,required" restrictions="*.fasta" /> | |
| <ITEM name="out" value="" type="string" description="Output idXML file." tags="output file,required" restrictions="*.IdXML" /> | |
| <ITEM name="decoy_string" value="REV_" type="string" description="String that was appended to the accession of the protein database to indicate a decoy protein." /> | |
| <ITEM name="write_protein_sequence" value="false" type="string" description="If set, the protein sequences are stored as well." restrictions="true,false" /> | |
| <ITEM name="prefix" value="true" type="string" description="If set, the decoy_string is supposed to be appended as a prefix." 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." restrictions="true,false" /> | |
| <ITEM name="allow_unmatched" value="true" type="string" description="If set, unmatched peptide sequences are allowed. By default (i.e. not set) the program terminates with error status on unmatched peptides." restrictions="true,false" /> | |
| <ITEM name="aaa_max" value="4" type="int" description="Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA's. AAA's are 'B', 'Z', and 'X'" restrictions="0:" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FalseDiscoveryRate" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="20" type="float" description="" /> | |
| <ITEM name="y_pos" value="-180" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Identification input file which contains a search against a concatenated sequence database" tags="input file" restrictions="*.idXML" /> | |
| <ITEM name="fwd_in" value="" type="string" description="Identification input to estimate FDR, forward" tags="input file" restrictions="*.idXML" /> | |
| <ITEM name="rev_in" value="" type="string" description="Identification input to estimate FDR, decoy run" tags="input file" restrictions="*.idXML" /> | |
| <ITEM name="out" value="" type="string" description="Identification output with annotated FDR" tags="output file,required" restrictions="*.idXML" /> | |
| <ITEM name="proteins_only" value="false" type="string" description="If set, the FDR of the proteins only is calculated" restrictions="true,false" /> | |
| <ITEM name="peptides_only" value="false" type="string" description="If set, the FDR of the peptides only is calculated" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameter section for the FDR calculation algorithm"> | |
| <ITEM name="q_value" value="true" type="string" description="If 'true', the q-values will be calculated instead of the FDRs" 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)" restrictions="true,false" /> | |
| <ITEM name="split_charge_variants" value="false" type="string" description="If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." restrictions="true,false" /> | |
| <ITEM name="treat_runs_separately" value="false" type="string" description="If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." restrictions="true,false" /> | |
| <ITEM name="decoy_string" value="REV_" type="string" description="String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only)." /> | |
| <ITEM name="add_decoy_peptides" value="false" type="string" description="If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score." restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="IDFilter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="20" type="float" description="" /> | |
| <ITEM name="y_pos" value="20" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file " tags="input file,required" restrictions="*.idXML" /> | |
| <ITEM name="out" value="" type="string" description="output file " tags="output file,required" restrictions="*.idXML" /> | |
| <ITEM name="min_length" value="0" type="int" description="Keep only peptide hits with a length greater or equal this value." restrictions="0:" /> | |
| <ITEM name="unique" value="false" type="string" description="If a peptide hit occurs more than once, only one instance is kept. This will (for instance) remove redundant identifications from multiple charge states or concurrent CID+HCD spectra. If you are aiming towards quantitation, you probably do *not* want to use this flag!" 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!" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="score" description="Filtering by peptide/protein score"> | |
| <ITEM name="pep" value="0.01" type="float" description="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc." /> | |
| <ITEM name="prot" value="0" type="float" description="The score which should be reached by a protein hit to be kept." /> | |
| </NODE> | |
| <NODE name="thresh" description="Filtering by significance threshold"> | |
| <ITEM name="pep" value="0" type="float" description="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." /> | |
| <ITEM name="prot" value="0" type="float" description="Keep a protein hit only if its score is above this fraction of the protein significance threshold." /> | |
| </NODE> | |
| <NODE name="whitelist" description="Filtering by whitelisting (only instances also present in a whitelist file can pass)"> | |
| <ITEM name="proteins" value="" type="string" description="filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are removed#br#All proteins whose accession is not present in this file are removed." tags="input file" restrictions="*.FASTA" /> | |
| <ITEM name="by_seq_only" value="false" type="string" description="Match peptides with FASTA file by sequence instead of accession and disable protein filtering." restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="blacklist" description="Filtering by blacklisting (only instances not present in a blacklist file can pass)"> | |
| <ITEM name="peptides" value="" type="string" description="Peptides having the same sequence as any peptide in this file will be filtered out#br#" tags="input file" restrictions="*.idXML" /> | |
| </NODE> | |
| <NODE name="rt" description="Filtering by RT predicted by 'RTPredict'"> | |
| <ITEM name="p_value" value="0" type="float" description="Retention time filtering by the p-value predicted by RTPredict." restrictions="0:1" /> | |
| <ITEM name="p_value_1st_dim" value="0" type="float" description="Retention time filtering by the p-value predicted by RTPredict for first dimension." restrictions="0:1" /> | |
| </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)." restrictions="0:" /> | |
| <ITEM name="n_protein_hits" value="0" type="int" description="Keep only the 'n' highest scoring protein hits (for n>0)." 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 two or more highest scoring hits, none are kept." restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <ITEM name="recycle_output" value="true" type="string" description="" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" /> | |
| <ITEMLIST name="file_names" type="string" description=""> | |
| <LISTITEM value="DEC_Yeast_orf_060512db.fasta"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-220" type="float" description="" /> | |
| <ITEM name="y_pos" value="-820" type="float" description="" /> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="SILACAnalyzer" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="280" type="float" description="" /> | |
| <ITEM name="y_pos" value="-640" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)" tags="input file,required" restrictions="*.mzML" /> | |
| <ITEM name="out" value="" type="string" 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." tags="output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_clusters" value="" type="string" description="Optional debug output containing data points passing all filters, hence belonging to a SILAC pattern. Points of the same colour correspond to the mono-isotopic peak of the lightest peptide in a pattern." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_features" value="" type="string" description="Optional output file containing the individual peptide features in 'out'." tags="advanced,output file" restrictions="*.featureXML" /> | |
| <ITEM name="out_filters" value="" type="string" description="Optional output file containing all points that passed the filters as txt. Suitable as input for 'in_filters' to perform clustering without preceding filtering process." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="in_filters" value="" type="string" description="Optional input file containing all points that passed the filters as txt. Use output from 'out_filters' to perform clustering only." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_debug" value="" type="string" description="Filename base for debug output." tags="advanced" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameters for the algorithm."> | |
| <ITEM name="allow_missing_peaks" value="true" type="string" description="Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Should such peptides be included in the analysis?" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="rt_threshold" value="30" type="float" 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.)" restrictions="0:" /> | |
| <ITEM name="rt_min" value="1" type="float" description="Lower bound for the retention time [s]." restrictions="0:" /> | |
| <ITEM name="intensity_cutoff" value="10000" type="float" description="Lower bound for the intensity of isotopic peaks in a SILAC pattern." restrictions="0:" /> | |
| <ITEM name="intensity_correlation" value="0.6" type="float" description="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." restrictions="0:1" /> | |
| <ITEM name="model_deviation" value="5" type="float" description="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation )." restrictions="1:" /> | |
| </NODE> | |
| <NODE name="labels" description="Isotopic labels that can be specified in section 'sample'."> | |
| <ITEM name="Arg6" value="6.0201290268" type="float" description="Arg6 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Arg10" value="10.0082686" type="float" description="Arg10 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys4" value="4.0251069836" type="float" description="Lys4 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys6" value="6.0201290268" type="float" description="Lys6 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys8" value="8.0141988132" type="float" description="Lys8 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL4" value="4.025107" type="float" description="mass difference between isotope-coded protein labels ICPL 4 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL6" value="6.020129" type="float" description="mass difference between isotope-coded protein labels ICPL 6 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL10" value="10.045236" type="float" description="mass difference between isotope-coded protein labels ICPL 10 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl4" value="4.0202" type="float" description="Methyl4 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl8" value="8.0202" type="float" description="Methyl8 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl12" value="12.0202" type="float" description="Methyl12 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl16" value="16.0202" type="float" description="Methyl16 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl24" value="24.0202" type="float" description="Methyl24 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl32" value="32.0202" type="float" description="Methyl32 mass shift" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="sample" description="Parameters describing the sample and its labels."> | |
| <ITEM name="labels" value="[Lys8,Arg10]" type="string" description="Labels used for labelling the sample. [...] specifies the labels for a single sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. For permitted labels see 'advanced parameters', section 'labels'. If left empty the tool identifies singlets, i.e. acts as peptide feature finder." /> | |
| <ITEM name="charge" value="1:5" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." /> | |
| <ITEM name="missed_cleavages" value="2" type="int" description="Maximum number of missed cleavages." restrictions="0:" /> | |
| <ITEM name="peaks_per_peptide" value="3:6" type="string" description="Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="IDMapper" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="280" type="float" description="" /> | |
| <ITEM name="y_pos" value="20" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="id" value="" type="string" description="Protein/peptide identifications file" tags="input file,required" restrictions="*.idXML" /> | |
| <ITEM name="in" value="" type="string" description="Feature map/consensus map file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="Output file (the format depends on the input file format)." tags="output file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="rt_tolerance" value="20" type="float" 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." restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="10" type="float" 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." restrictions="0:" /> | |
| <ITEM name="mz_measure" value="ppm" type="string" description="Unit of 'mz_tolerance'." 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 'use_centroid_mz' to avoid false-positive matches.)" 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." restrictions="true,false" /> | |
| <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." 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.)" restrictions="true,false" /> | |
| <ITEM name="use_subelements" value="true" 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." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="ProteinQuantifier" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="280" type="float" description="" /> | |
| <ITEM name="y_pos" value="200" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Input file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="protxml" value="" type="string" description="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." tags="input file" restrictions="*.idXML" /> | |
| <ITEM name="out" value="" type="string" description="Output file for protein abundances" tags="output file" /> | |
| <ITEM name="peptide_out" value="" type="string" description="Output file for peptide abundances" tags="output file" /> | |
| <ITEM name="id_out" value="" type="string" description="Output file for peptide and protein abundances (annotated idXML) - suitable for export to mzTab.#br#Either 'out', 'peptide_out', or 'id_out' are required. They can be used together." tags="output file" restrictions="*.idXML" /> | |
| <ITEM name="top" value="1" type="int" description="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" restrictions="0:" /> | |
| <ITEM name="average" value="median" type="string" description="Averaging method used to compute protein abundances from peptide abundances" restrictions="median,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)" 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." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="consensus" description="Additional options for consensus maps"> | |
| <ITEM name="normalize" value="false" type="string" description="Scale peptide abundances so that medians of all samples are equal" 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!)." 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" /> | |
| <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" 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" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="edges" description=""> | |
| <NODE name="0" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="5/6" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/4" type="string" description="" /> | |
| </NODE> | |
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from old website's workflow section:
�SILAC analysis pipeline for Thermo Orbi XL data with Mascot identification
input [1]: mzML
input [3]: fasta database
output [10]: protein abundances
SILAC peptide pairs are detected in [4]. Sequences are identified in [2, 5-7].
Lars Nilse l.nilse@dunelm.org.uk