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June 8, 2016 12:59
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="1.10.0" type="string" description="" /> | |
| <ITEM name="num_vertices" value="13" type="int" description="" /> | |
| <ITEM name="num_edges" value="14" type="int" description="" /> | |
| <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> | |
| <html><head><meta name="qrichtext" content="1" /><style type="text/css"> | |
| p, li { white-space: pre-wrap; } | |
| </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;"> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">A labelfree ID and quantification pipeline.</span></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; font-family:'Sans Serif'; font-size:9pt;"><br /></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">Input node #1 should contain your input files (containing both MS1 and MS2 spectra)</span></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; font-family:'Sans Serif'; font-size:9pt;"><br /></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">Input node #2 should contain the database you want to search against. It should be a target-decoy-database. Otherwise, FDR filtering will not work. Moreover, you must specify the decoy string appended or prepended to the accessions of decoy sequences in your database in the parameters of PeptideIndexer.</span></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; font-family:'Sans Serif'; font-size:9pt;"><br /></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">In order for this to run, you must first download OMSSA and set the path to the executables in the parameters of the respective nodes.</span></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; font-family:'Sans Serif'; font-size:9pt;"><br /></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">IDMapper maps the FDR-filtered IDs to the MS1 features found by FeatureFinderCentroided. The annotated featureXML files are then aligned using MapAlignerPoseClustering and finally linked using FeatureLinkerUnlabeledQT.</span></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; font-family:'Sans Serif'; font-size:9pt;"><br /></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">Protein inference is performed by the ProteinQuantifier tool.</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">The final results are exported to mzTab.</span></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; font-family:'Sans Serif'; font-size:9pt;"><br /></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">(Note:</span></p> | |
| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans Serif'; font-size:9pt;">This pipeline has been successfully applied to data acquired on an Orbitrap Velos. Be sure to adapt the settings of the individual tools (RT and mass tolerance, considered charge states, ...) to fit your dataset.)</span></p></body></html>]]>" type="string" description="" /> | |
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| <NODE name="vertices" description=""> | |
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| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" /> | |
| <ITEMLIST name="file_names" type="string" description=""> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="20" type="float" description="" /> | |
| <ITEM name="y_pos" value="-80" type="float" description="" /> | |
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| <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="OMSSAAdapter" 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="220" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file (valid formats: 'mzML')" tags="input file,required" /> | |
| <ITEM name="out" value="" type="string" description="output file (valid formats: 'idXML')" tags="output file,required" /> | |
| <ITEM name="precursor_mass_tolerance" value="10" type="float" description="precursor mass tolerance (Default: Dalton)" /> | |
| <ITEM name="precursor_mass_tolerance_unit_ppm" value="true" type="string" description="If this flag is set, ppm is used as precursor mass tolerance unit" restrictions="true,false" /> | |
| <ITEM name="fragment_mass_tolerance" value="0.5" type="float" description="fragment mass error in Dalton" /> | |
| <ITEM name="database" value="" type="string" description="NCBI formatted FASTA files. Only the .psq filename should be given, e.g. 'SwissProt.fasta.psq'. If the filename does not end in '.psq' the suffix will be added automatically. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'" tags="input file,required" /> | |
| <ITEM name="min_precursor_charge" value="2" type="int" description="minimum precursor ion charge" /> | |
| <ITEM name="max_precursor_charge" value="5" type="int" description="maximum precursor ion charge" /> | |
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(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 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(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="Carbamidomethyl (C)"/> | |
| </ITEMLIST> | |
| <ITEMLIST name="variable_modifications" type="string" description="variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'" 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="Oxidation (M)"/> | |
| </ITEMLIST> | |
| <ITEM name="omssa_executable" value="" type="string" description="The 'omssacl' executable of the OMSSA installation" tags="input file,required" /> | |
| <ITEM name="omssa_user_mods" value="" type="string" description="additional <MSModSpec> subtrees of user modifications.#br#Subtrees will be pasted into OMSSAAdapter generated user mod files.#br#See http://www.ncbi.nlm.nih.gov/data_specs/schema/OMSSA.mod.xsd for details about user mod file definition." tags="advanced,input file" /> | |
| <ITEM name="pc" value="1" type="int" description="The number of pseudocounts to add to each precursor mass bin" tags="advanced" /> | |
| <ITEM name="hs" value="4" type="int" description="the minimum number of m/z values a spectrum must have to be searched" tags="advanced" /> | |
| <ITEM name="tez" value="1" type="int" description="scaling of precursor mass tolerance with charge (0 = none, 1= linear)" tags="advanced" /> | |
| <ITEM name="tom" value="0" type="int" description="product ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" tags="advanced" /> | |
| <ITEM name="tem" value="0" type="int" description="precursor ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" tags="advanced" /> | |
| <ITEM name="tex" value="1446.94" type="float" description="threshold in Da above which the mass of a neutron should be added in an exact mass search" tags="advanced" /> | |
| <ITEM name="zt" value="3" type="int" description="minimum precursor charge to start considering multiply charged products" tags="advanced" /> | |
| <ITEM name="z1" value="0.95" type="float" description="the fraction of peaks below the precursor used to determine if the spectrum is charge +1" tags="advanced" /> | |
| <ITEM name="zc" value="1" type="int" description="should charge +1 be determined algorithmically (1=yes)" tags="advanced" /> | |
| <ITEM name="zcc" value="2" type="int" description="how should precursor charges be determined? (1=believe the input file,2=use the specified range)" tags="advanced" /> | |
| <ITEM name="zoh" value="2" type="int" description="set the maximum product charge to search" tags="advanced" /> | |
| <ITEM name="v" value="1" type="int" description="number of missed cleavages allowed" /> | |
| <ITEM name="e" value="0" type="int" description="id number of enzyme to use (trypsin is the default)" /> | |
| <ITEM name="no" value="4" type="int" description="minimum size of peptides for no-enzyme and semi-tryptic searches" tags="advanced" /> | |
| <ITEM name="nox" value="40" type="int" description="maximum size of peptides for no-enzyme and semi-tryptic searches" tags="advanced" /> | |
| <ITEM name="i" value="1,4" type="string" description="comma delimited list of id numbers of ions to search" tags="advanced" /> | |
| <ITEM name="sp" value="100" type="int" description="number of product ions to search" tags="advanced" /> | |
| <ITEM name="sb1" value="1" type="int" description="should first forward (e.g. b1) product ions be searched (1 = no, 0 = yes)" tags="advanced" /> | |
| <ITEM name="sct" value="0" type="int" description="should c terminus ions (e.g. y1) be searched (1 = no, 0 = yes)" tags="advanced" /> | |
| <ITEM name="x" value="0" type="string" description="comma delimited list of NCBI taxonomy ids to search (0 = all. This is the default)" tags="advanced" /> | |
| <ITEM name="hm" value="2" type="int" description="the minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded" tags="advanced" /> | |
| <ITEM name="ht" value="6" type="int" description="number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide" tags="advanced" /> | |
| <ITEM name="hl" value="10" type="int" description="maximum number of hits retained for one spectrum. Note: even when set to 1 OMSSA may report multiple hits with different charge states" /> | |
| <ITEM name="he" value="100000" type="float" description="the maximum e-value allowed in the hit list" /> | |
| <ITEM name="mm" value="128" type="int" description="the maximum number of mass ladders to generate per database peptide" tags="advanced" /> | |
| <ITEM name="mnm" value="false" type="string" description="n-term methionine should not be cleaved" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="is" value="0" type="float" description="evalue threshold to include a sequence in the iterative search, 0 = all" tags="advanced" /> | |
| <ITEM name="ir" value="0" type="float" description="evalue threshold to replace a hit, 0 = only if better" tags="advanced" /> | |
| <ITEM name="ii" value="0" type="float" description="evalue threshold to iteratively search a spectrum again, 0 = always" 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> | |
| </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="400" type="float" description="" /> | |
| <ITEM name="y_pos" value="220" 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 (valid formats: 'idXML')" tags="input file" /> | |
| <ITEM name="fwd_in" value="" type="string" description="Identification input to estimate FDR, forward (valid formats: 'idXML')" tags="input file" /> | |
| <ITEM name="rev_in" value="" type="string" description="Identification input to estimate FDR, decoy run (valid formats: 'idXML')" tags="input file" /> | |
| <ITEM name="out" value="" type="string" description="Identification output with annotated FDR" tags="output file,required" /> | |
| <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="580" type="float" description="" /> | |
| <ITEM name="y_pos" value="220" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file (valid formats: 'idXML')" tags="input file,required" /> | |
| <ITEM name="out" value="" type="string" description="output file (valid formats: 'idXML')" tags="output file,required" /> | |
| <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. (valid formats: 'FASTA')" tags="input file" /> | |
| <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#(valid formats: 'idXML')" tags="input file" /> | |
| </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="1" 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=""> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="120" type="float" description="" /> | |
| <ITEM name="y_pos" value="340" type="float" description="" /> | |
| </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="220" type="float" description="" /> | |
| <ITEM name="y_pos" value="220" 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" /> | |
| <ITEM name="out" value="" type="string" description="Output idXML file." tags="output file,required" /> | |
| <ITEM name="decoy_string" value="IPI: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="false" 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="9" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="MapAlignerPoseClustering" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="500" type="float" description="" /> | |
| <ITEM name="y_pos" value="520" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="string" description="Input files separated by blanks (all must have the same file type)" tags="input file,required" restrictions="*.mzML,*.featureXML"> | |
| </ITEMLIST> | |
| <ITEMLIST name="out" type="string" description="Output files separated by blanks" tags="output file" restrictions="*.mzML,*.featureXML"> | |
| </ITEMLIST> | |
| <ITEMLIST name="trafo_out" type="string" description="Transformation output files separated by blanks" tags="output file" restrictions="*.trafoXML"> | |
| </ITEMLIST> | |
| <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="reference" description="Options to define a reference file"> | |
| <ITEM name="file" value="" type="string" description="File to use as reference (same file format as input files required)" tags="input file" restrictions="*.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." restrictions="0:" /> | |
| </NODE> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="max_num_peaks_considered" value="400" type="int" description="The maximal number of peaks to be considered per map. This cutoff is only applied to peak maps. To use all peaks, set this to '-1'." restrictions="-1:" /> | |
| <NODE name="superimposer" description=""> | |
| <ITEM name="mz_pair_max_distance" value="0.001" type="float" description="Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing." restrictions="0:" /> | |
| <ITEM name="rt_pair_distance_fraction" value="0.1" type="float" 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). " tags="advanced" restrictions="0:1" /> | |
| <ITEM name="num_used_points" value="1000" 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." restrictions="-1:" /> | |
| <ITEM name="scaling_bucket_size" value="0.005" type="float" 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." restrictions="0:" /> | |
| <ITEM name="shift_bucket_size" value="3" type="float" 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." restrictions="0:" /> | |
| <ITEM name="max_shift" value="1000" type="float" description="Maximal shift which is considered during histogramming. This applies for both directions." tags="advanced" restrictions="0:" /> | |
| <ITEM name="max_scaling" value="2" type="float" description="Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this." tags="advanced" 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." tags="advanced" /> | |
| <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." tags="advanced" /> | |
| </NODE> | |
| <NODE name="pairfinder" description=""> | |
| <ITEM name="second_nearest_gap" value="2" type="float" description="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself" restrictions="1:" /> | |
| <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)" restrictions="true,false" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="60" type="float" description="Maximum allowed difference in RT" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="float" description="Normalized RT differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="RT distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="10" type="float" description="Maximum allowed difference in m/z (unit defined by 'mz_unit')" restrictions="0:" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Unit of the 'max_difference' parameter" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="float" description="Normalized m/z differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="m/z distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity"> | |
| <ITEM name="exponent" value="1" type="float" description="Differences in relative intensity are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="float" description="Distances based on relative intensity are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="model" description="Options to control the modeling of retention time transformations from data"> | |
| <ITEM name="type" value="linear" type="string" description="Type of model" restrictions="linear,b_spline,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'." restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="b_spline" description="Parameters for 'b_spline' model"> | |
| <ITEM name="num_breakpoints" value="5" type="int" description="Number of breakpoints of the cubic spline in the smoothing step. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape." restrictions="2:" /> | |
| <ITEM name="break_positions" value="uniform" type="string" description="How to distribute the breakpoints on the retention time scale. 'uniform': intervals of equal size; 'quantiles': equal number of data points per interval." restrictions="uniform,quantiles" /> | |
| </NODE> | |
| <NODE name="interpolated" description="Parameters for 'interpolated' model"> | |
| <ITEM name="interpolation_type" value="cspline" type="string" description="Type of interpolation to apply." restrictions="linear,cspline,akima" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FeatureLinkerUnlabeledQT" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="260" type="float" description="" /> | |
| <ITEM name="y_pos" value="520" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="string" description="input files separated by blanks" tags="input file,required" restrictions="*.featureXML,*.consensusXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="string" description="Output file" tags="output file,required" restrictions="*.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." 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="Algorithm parameters section"> | |
| <ITEM name="use_identifications" value="true" type="string" description="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." restrictions="true,false" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="60" type="float" description="Maximum allowed difference in RT" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="float" description="Normalized RT differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="RT distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="10" type="float" description="Maximum allowed difference in m/z (unit defined by 'mz_unit')" restrictions="0:" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Unit of the 'max_difference' parameter" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="float" description="Normalized m/z differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="m/z distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity"> | |
| <ITEM name="exponent" value="1" type="float" description="Differences in relative intensity are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="float" description="Distances based on relative intensity are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| </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="700" type="float" description="" /> | |
| <ITEM name="y_pos" value="380" 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="60" 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="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." 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="merger" type="string" description="" /> | |
| <ITEM name="x_pos" value="700" type="float" description="" /> | |
| <ITEM name="y_pos" value="520" type="float" description="" /> | |
| <ITEM name="round_based" value="false" type="string" description="" /> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="20" type="float" description="" /> | |
| <ITEM name="y_pos" value="700" type="float" description="" /> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FeatureFinderCentroided" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="820" type="float" description="" /> | |
| <ITEM name="y_pos" value="220" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file" tags="input file,required" restrictions="*.mzML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.featureXML" /> | |
| <ITEM name="seeds" value="" type="string" description="User specified seed list" tags="input file" restrictions="*.featureXML" /> | |
| <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="Algorithm section"> | |
| <ITEM name="debug" value="false" type="string" description="When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode)." restrictions="true,false" /> | |
| <NODE name="intensity" description="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)"> | |
| <ITEM name="bins" value="10" type="int" description="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map." restrictions="1:" /> | |
| </NODE> | |
| <NODE name="mass_trace" description="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1)."> | |
| <ITEM name="mz_tolerance" value="0.01" type="float" description="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instument.#br#This value must be smaller than that 1/charge_high!" restrictions="0:" /> | |
| <ITEM name="min_spectra" value="8" type="int" description="Number of spectra that have to show a similar peak mass in a mass trace." restrictions="1:" /> | |
| <ITEM name="max_missing" value="2" type="int" description="Number of consecutive spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below 'min_spectra'!" restrictions="0:" /> | |
| <ITEM name="slope_bound" value="1" type="float" description="The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to seperate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot." restrictions="0:" /> | |
| </NODE> | |
| <NODE name="isotopic_pattern" description="Settings for the calculation of a score indicating if a peak is part of a isotoipic pattern (between 0 and 1)."> | |
| <ITEM name="charge_low" value="2" type="int" description="Lowest charge to search for." restrictions="1:" /> | |
| <ITEM name="charge_high" value="4" type="int" description="Highest charge to search for." restrictions="1:" /> | |
| <ITEM name="mz_tolerance" value="0.01" type="float" description="Tolerated m/z deviation from the theoretical isotopic pattern.#br#It should be larger than the m/z resolution of the instument.#br#This value must be smaller than that 1/charge_high!" restrictions="0:" /> | |
| <ITEM name="intensity_percentage" value="10" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="intensity_percentage_optional" value="0.1" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="optional_fit_improvement" value="2" type="float" description="Minimal percental improvement of isotope fit to allow leaving out an optional peak." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="mass_window_width" value="25" type="float" description="Window width in Dalton for precalculation of estimated isotope distribtions." tags="advanced" restrictions="1:200" /> | |
| </NODE> | |
| <NODE name="seed" description="Settings that determine which peaks are considered a seed"> | |
| <ITEM name="min_score" value="0.5" type="float" description="Minimum seed score a peak has to reach to be used as seed.#br#The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.#br#If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score." restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="fit" description="Settings for the model fitting"> | |
| <ITEM name="epsilon_abs" value="0.0001" type="float" description="Absolute epsilon used for convergence of the fit." tags="advanced" restrictions="0:" /> | |
| <ITEM name="epsilon_rel" value="0.0001" type="float" description="Relative epsilon used for convergence of the fit." tags="advanced" restrictions="0:" /> | |
| <ITEM name="max_iterations" value="500" type="int" description="Maximum number of iterations of the fit." tags="advanced" restrictions="1:" /> | |
| </NODE> | |
| <NODE name="feature" description="Settings for the features (intensity, quality assessment, ...)"> | |
| <ITEM name="min_score" value="0.5" type="float" description="Feature score threshold for a feature to be reported.#br#The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks." restrictions="0:1" /> | |
| <ITEM name="min_isotope_fit" value="0.8" type="float" description="Minimum isotope fit of the feature before model fitting." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="min_trace_score" value="0.5" type="float" description="Trace score threshold.#br#Traces below this threshold are removed after the model fitting.#br#This parameter is important for features that overlap in m/z dimension." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="min_rt_span" value="0.333" type="float" description="Minimum RT span in relation to extended area that has to remain after model fitting." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="max_rt_span" value="2.5" type="float" description="Maximum RT span in relation to extended area that the model is allowed to have." tags="advanced" restrictions="0.5:" /> | |
| <ITEM name="rt_shape" value="symmetric" type="string" description="Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used." tags="advanced" restrictions="symmetric,asymmetric" /> | |
| <ITEM name="max_intersection" value="0.35" type="float" description="Maximum allowed intersection of features." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="reported_mz" value="monoisotopic" type="string" description="The mass type that is reported for features.#br#'maximum' returns the m/z value of the highest mass trace.#br#'average' returns the intensity-weighted average m/z value of all contained peaks.#br#'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model." restrictions="maximum,average,monoisotopic" /> | |
| </NODE> | |
| <NODE name="user-seed" description="Settings for user-specified seeds."> | |
| <ITEM name="rt_tolerance" value="30" type="float" description="Allowed RT deviation of seeds from the user-specified seed position." restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="0.1" type="float" description="Allowed m/z deviation of seeds from the user-specified seed position." restrictions="0:" /> | |
| <ITEM name="min_score" value="0.5" type="float" description="Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case." restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="debug" description=""> | |
| <ITEM name="pseudo_rt_shift" value="500" type="float" description="Pseudo RT shift used when ." tags="advanced" restrictions="1:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" 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="20" type="float" description="" /> | |
| <ITEM name="y_pos" value="520" 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="mzTab_out" value="" type="string" description="Export to mzTab.#br#Either 'out', 'peptide_out', or 'mzTab_out' are required. They can be used together." tags="output file" /> | |
| <ITEM name="top" value="3" 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="ratios" value="false" type="string" description="Prints the log2 ratios of the abundance value to the output file. (log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) ....)" restrictions="true,false" /> | |
| <ITEM name="ratiosSILAC" value="false" type="string" description="Prints the SILAC log2 ratios for a triple SILAC experiment to the output file. Only performed if three maps are given, otherwise nothing will be seen in the output file. (log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)" 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="0/3" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" 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="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="2" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/3" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="database" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="4/5" 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="4" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/4" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="fasta" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="9/10" 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="6" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="7/8" 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="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="8/9" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="6/7" 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="id" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/2" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/7" 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="11" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="10/11" 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="12" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="11/12" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="mzTab_out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/4" 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> | |
| </PARAMETERS> |
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from old website's workflow section:
�A labelfree ID and quantification pipeline.
Input node #1 should contain your input files (containing both MS1 and MS2 spectra)
Input node #2 should contain the database you want to search against. It should be a target-decoy-database. Otherwise, FDR filtering will not work. Moreover, you must specify the decoy string appended or prepended to the accessions of decoy sequences in your database in the parameters of PeptideIndexer.
In order for this to run, you must first download OMSSA and set the path to the executables in the parameters of the respective nodes.
IDMapper maps the FDR-filtered IDs to the MS1 features found by FeatureFinderCentroided. The annotated featureXML files are then aligned using MapAlignerPoseClustering and finally linked using FeatureLinkerUnlabeledQT.
Protein inference is performed by the ProteinQuantifier tool.
The final results are exported to mzTab.
(Note: This pipeline has been successfully applied to data acquired on an Orbitrap Velos. Be sure to adapt the settings of the individual tools (RT and mass tolerance, considered charge states, ...) to fit your dataset.)