Mercurial > repos > galaxyp > maxquant
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit c810d2eaedfcad1edf1a84cab8296dcd7b35f5bc
| author | galaxyp |
|---|---|
| date | Mon, 18 Mar 2024 13:07:04 +0000 |
| parents | 8934bc76bb52 |
| children |
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<?xml version="1.0" ?> <macros> <token name="@PROFILE@">21.05</token> <token name="@VERSION@">2.0.3.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@VERSION_SUFFIX_MQPAR@">0</token> <token name="@VERSION_PTXQC@">1.0.16</token> <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> <token name="@TMT2PLEX@"> - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] </token> <token name="@TMT6PLEX@"> - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True] - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True] - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True] - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True] - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True] - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True] </token> <token name="@TMT8PLEX@"> - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True] - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True] - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True] - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True] - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True] - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True] - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True] - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True] </token> <token name="@TMT10PLEX@"> - [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True] - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True] - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True] - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True] - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True] - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True] - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True] - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True] - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True] - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True] </token> <token name="@TMT11PLEX@"> @TMT10PLEX@ - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True] </token> <token name="@TMTPRO16PLEX@"> - [TMTpro16plex-Lys127N,TMTpro16plex-Nter127N,0,0,0,0,True] - [TMTpro16plex-Lys127C,TMTpro16plex-Nter127C,0,0,0,0,True] - [TMTpro16plex-Lys128N,TMTpro16plex-Nter128N,0,0,0,0,True] - [TMTpro16plex-Lys128C,TMTpro16plex-Nter128C,0,0,0,0,True] - [TMTpro16plex-Lys129N,TMTpro16plex-Nter129N,0,0,0,0,True] - [TMTpro16plex-Lys129C,TMTpro16plex-Nter129C,0,0,0,0,True] - [TMTpro16plex-Lys130N,TMTpro16plex-Nter130N,0,0,0,0,True] - [TMTpro16plex-Lys130C,TMTpro16plex-Nter130C,0,0,0,0,True] - [TMTpro16plex-Lys131N,TMTpro16plex-Nter131N,0,0,0,0,True] - [TMTpro16plex-Lys131C,TMTpro16plex-Nter131C,0,0,0,0,True] - [TMTpro16plex-Lys132N,TMTpro16plex-Nter132N,0,0,0,0,True] - [TMTpro16plex-Lys132C,TMTpro16plex-Nter132C,0,0,0,0,True] - [TMTpro16plex-Lys133N,TMTpro16plex-Nter133N,0,0,0,0,True] - [TMTpro16plex-Lys133C,TMTpro16plex-Nter133C,0,0,0,0,True] - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True] - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True] </token> <token name="@TMTPRO18PLEX@"> @TMTPRO16PLEX@ - [TMTpro18plex-Lys134C,TMTpro18plex-Nter134C,0,0,0,0,True] - [TMTpro18plex-Lys135N,TMTpro18plex-Nter135N,0,0,0,0,True] </token> <token name="@ITRAQ4PLEX@"> - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] </token> <token name="@ITRAQ8PLEX@"> - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False] @ITRAQ4PLEX@ - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False] - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False] - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False] </token> <token name="@IODOTMT6PLEX@"> - [iodoTMT6plex-Cys126,'',0,0,0,0,True] - [iodoTMT6plex-Cys127,'',0,0,0,0,True] - [iodoTMT6plex-Cys128,'',0,0,0,0,True] - [iodoTMT6plex-Cys129,'',0,0,0,0,True] - [iodoTMT6plex-Cys130,'',0,0,0,0,True] - [iodoTMT6plex-Cys131,'',0,0,0,0,True] </token> <xml name="xrefs"> <xrefs> <xref type="bio.tools">maxquant</xref> </xrefs> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">maxquant</requirement> <requirement type="package" version="5.4.1">pyyaml</requirement> <requirement type="package" version="3.1.418">dotnet</requirement> <requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement> <requirement type="package" version="1.32">tar</requirement> </requirements> </xml> <xml name="required_files"> <required_files> <include path="create_mqpar.py" /> <include path="modify_mqpar.py" /> <include path="mqparam.py" /> </required_files> </xml> <xml name="ptxqc"> <configfile name="qr_yaml"> PTXQC: ReportFilename: extended: yes UseLocalMQPar: yes NameLengthMax_num: 10.0 OutputFormats: - plainPDF PlainPDF: AddPageNumbers: 'on' File: Parameters: #if $qc.do_it == "true": enabled: ${qc.parameters} #end if Summary: #if $qc.do_it == "true": enabled: ${qc.summary} #end if IDRate: Thresh_bad_num: 20.0 Thresh_great_num: 35.0 ProteinGroups: #if $qc.do_it == "true": enabled: ${qc.proteingroups} #end if RatioPlot: LabelIncThresh_num: 4.0 IntensityThreshLog2_num: 25.0 Evidence: #if $qc.do_it == "true": enabled: ${qc.evidence} #end if ProteinCountThresh_num: 3500.0 IntensityThreshLog2_num: 23.0 PeptideCountThresh_num: 15000.0 SpecialContaminants: cont_MYCO: - MYCOPLASMA - '1' #if $varExists("mqpar_input"): #import re #set $mqpar_xml = open(str($mqpar_input), "r").read() #set $matchingTimeWindow = re.search("matchingTimeWindow>(.*)./matchingTimeWindow", $mqpar_xml).group(1) MQpar_MatchingTimeWindow_num: ${matchingTimeWindow} #else: #if $search_opts.mbr.match_between_runs == 'True': MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window} #else: MQpar_MatchingTimeWindow_num: 0.0 #end if #end if MatchBetweenRuns_wA: auto MQpar_firstSearchTol_num: 20.0 firstSearch_outOfCalWarnSD_num: 2.0 MQpar_mainSearchTol_num: 4.5 MsMs: #if $qc.do_it == "true": enabled: ${qc.msms} #end if MsMsScans: #if $qc.do_it == "true": enabled: ${qc.msmsscans} #end if IonInjectionThresh_num: 10.0 order: qcMetric_PAR: 1.0 qcMetric_PG_PCA: 3.0 qcMetric_EVD_Top5Cont: 10.0 qcMetric_PG_Ratio: 19.0 qcMetric_EVD_UserContaminant: 20.0 qcMetric_EVD_PeptideInt: 30.0 qcMetric_EVD_ReporterInt: 31.0 qcMetric_PG_RawInt: 32.0 qcMetric_PG_LFQInt: 33.0 qcMetric_PG_ReporterInt: 34.0 qcMetric_MSMS_MissedCleavages: 40.0 qcMetric_EVD_Charge: 100.0 qcMetric_PG_Cont: 110.0 qcMetric_MSMSScans_TopNoverRT: 120.0 qcMetric_EVD_IDoverRT: 150.0 qcMetric_EVD_RTPeakWidth: 170.0 qcMetric_EVD_MBRAlign: 210.0 qcMetric_EVD_MBRIdTransfer: 220.0 qcMetric_EVD_MBRaux: 221.0 qcMetric_MSMSScans_IonInjTime: 240.0 qcMetric_MSMSScans_MSMSIntensity: 245.0 qcMetric_EVD_MS2OverSampling: 250.0 qcMetric_EVD_PreCal: 260.0 qcMetric_EVD_PostCal: 270.0 qcMetric_MSMS_MSMSDecal: 280.0 qcMetric_SM_MSMSIdRate: 300.0 qcMetric_MSMSScans_TopNID: 380.0 qcMetric_MSMSScans_DepPep: 383.0 qcMetric_EVD_MissingValues: 390.0 qcMetric_EVD_PeptideCount: 400.0 qcMetric_EVD_ProteinCount: 450.0 qcMetric_AverageQualOverall: 9999.0 </configfile> <configfile name="qr"> library(PTXQC) library(data.table) library(yaml) library(methods) args = commandArgs(trailingOnly=TRUE) yaml_config = yaml.load_file(input = args[1]) r = createReport('./combined/txt', yaml_obj=yaml_config) cat(paste0("\nReport generated as '", r\$report_file, "'\n\n")) </configfile> </xml> <xml name="mod_option" token_value="default"> <option value="@VALUE@">@VALUE@</option> </xml> <xml name="default_mod_option" token_value="default"> <option selected="true" value="@VALUE@">@VALUE@</option> </xml> <xml name="ptxqc-opts"> <conditional name="qc"> <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="select"> <option value="true">True</option> <option value="false" selected="true">False</option> </param> <when value="true"> <param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/> <param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/> <param name="proteingroups" type="boolean" checked="true" label="use proteinGroups.txt?" truevalue="yes" falsevalue="no"/> <param name="evidence" type="boolean" checked="true" label="use evidence.txt?" truevalue="yes" falsevalue="no"/> <param name="msms" type="boolean" checked="true" label="use msms.txt?" truevalue="yes" falsevalue="no"/> <param name="msmsscans" type="boolean" checked="true" label="use msmsScans.txt?" truevalue="yes" falsevalue="no"/> </when> <when value="false"/> </conditional> </xml> <xml name="output" tokens="name,label" token_format="tabular"> <data format="@FORMAT@" label="${on_string}: @LABEL@" name="@NAME@"> <filter>'@NAME@' in output_opts['output']</filter> </data> </xml> <xml name="output_from_wdir" tokens="name,label" token_ext="txt" token_format="tabular"> <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="${on_string}: @LABEL@" name="@NAME@"> <filter>'@NAME@' in output_opts['output']</filter> </data> </xml> <xml name="outputs"> <outputs> <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/> <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/> <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/> <expand macro="output_from_wdir" name="evidence" label="MaxQuant Evidence"/> <expand macro="output_from_wdir" name="parameters" label="MaxQuant Tabular Parameters"/> <expand macro="output_from_wdir" name="msms" label="MaxQuant MSMS"/> <expand macro="output_from_wdir" name="mzTab" label="mzTab" format="mztab" ext="mzTab"/> <expand macro="output_from_wdir" name="allPeptides" label="all peptides"/> <expand macro="output_from_wdir" name="libraryMatch" label="library match"/> <expand macro="output_from_wdir" name="matchedFeatures" label="matched features"/> <expand macro="output_from_wdir" name="modificationSpecificPeptides" label="modification specific peptides"/> <expand macro="output_from_wdir" name="ms3Scans" label="ms3 scans"/> <expand macro="output_from_wdir" name="msmsScans" label="msms Scans"/> <expand macro="output_from_wdir" name="mzRange" label="mz range"/> <expand macro="output_from_wdir" name="peptideSection" label="peptide section"/> <expand macro="output_from_wdir" name="summary" label="MaxQuant summary"/> <expand macro="output" name="output_all" format="tar" label="'combined/txt/' directory"/> <expand macro="output" name="log" format="txt" label="log"/> <expand macro="output" name="config" format="txt" label="yaml config file"/> <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report"> <filter>qc['do_it'] == "true"</filter> </data> </outputs> </xml> <xml name="modification"> <expand macro="mod_option" value="Acetyl (K)"/> <expand macro="mod_option" value="Phospho (STY)"/> <expand macro="mod_option" value="GlyGly (K)"/> <expand macro="mod_option" value="Methyl (KR)"/> <expand macro="mod_option" value="Dimethyl (KR)"/> <expand macro="mod_option" value="Trimethyl (K)"/> <expand macro="mod_option" value="Pro5"/> <expand macro="mod_option" value="Pro6"/> <expand macro="mod_option" value="Glu->pyro-Glu"/> <expand macro="mod_option" value="Gln->pyro-Glu"/> <expand macro="mod_option" value="QQTGG (K)"/> <expand macro="mod_option" value="Deamidation (N)"/> <expand macro="mod_option" value="Deamidation 18O (N)"/> <expand macro="mod_option" value="Deamidation (NQ)"/> <expand macro="mod_option" value="Hydroxyproline"/> <expand macro="mod_option" value="Carbamyl (N-term)"/> <expand macro="mod_option" value="Delta:H(2)C(2) (N-term)"/> <expand macro="mod_option" value="Dioxidation (MW)"/> <expand macro="mod_option" value="Trioxidation (C)"/> <expand macro="mod_option" value="Dethiomethyl (M)"/> <expand macro="mod_option" value="Cation:Na (DE)"/> <expand macro="mod_option" value="Methyl (E)"/> <expand macro="mod_option" value="Dehydrated (ST)"/> <expand macro="mod_option" value="Oxidation (P)"/> <expand macro="mod_option" value="Dimethyl (K)"/> <expand macro="mod_option" value="Amidated (Protein C-term)"/> <expand macro="mod_option" value="Sulfo (STY)"/> <expand macro="mod_option" value="Acetyl (N-term)"/> <expand macro="mod_option" value="Amidated (C-term)"/> <expand macro="mod_option" value="Sulfation (Y)"/> <expand macro="mod_option" value="Phospho (ST)"/> <expand macro="mod_option" value="Cys-Cys"/> <expand macro="mod_option" value="Ala->Arg"/> <expand macro="mod_option" value="Ala->Asn"/> <expand macro="mod_option" value="Ala->Asp"/> <expand macro="mod_option" value="Ala->Cys"/> <expand macro="mod_option" value="Ala->Gln"/> <expand macro="mod_option" value="Ala->Glu"/> <expand macro="mod_option" value="Ala->Gly"/> <expand macro="mod_option" value="Ala->His"/> <expand macro="mod_option" value="Ala->Xle"/> <expand macro="mod_option" value="Ala->Lys"/> <expand macro="mod_option" value="Ala->Met"/> <expand macro="mod_option" value="Ala->Phe"/> <expand macro="mod_option" value="Ala->Pro"/> <expand macro="mod_option" value="Ala->Ser"/> <expand macro="mod_option" value="Ala->Thr"/> <expand macro="mod_option" value="Ala->Trp"/> <expand macro="mod_option" value="Ala->Tyr"/> <expand macro="mod_option" value="Ala->Val"/> <expand macro="mod_option" value="Arg->Ala"/> <expand macro="mod_option" value="Arg->Asn"/> <expand macro="mod_option" value="Arg->Asp"/> <expand macro="mod_option" value="Arg->Cys"/> <expand macro="mod_option" value="Arg->Gln"/> <expand macro="mod_option" value="Arg->Glu"/> <expand macro="mod_option" value="Arg->Gly"/> <expand macro="mod_option" value="Arg->His"/> <expand macro="mod_option" value="Arg->Lys"/> <expand macro="mod_option" value="Arg->Met"/> <expand macro="mod_option" value="Arg->Phe"/> <expand macro="mod_option" value="Arg->Pro"/> <expand macro="mod_option" value="Arg->Ser"/> <expand macro="mod_option" value="Arg->Thr"/> <expand macro="mod_option" value="Arg->Trp"/> <expand macro="mod_option" value="Arg->Tyr"/> <expand macro="mod_option" value="Arg->Val"/> <expand macro="mod_option" value="Arg->Xle"/> <expand macro="mod_option" value="Asn->Ala"/> <expand macro="mod_option" value="Asn->Arg"/> <expand macro="mod_option" value="Asn->Asp"/> <expand macro="mod_option" value="Asn->Cys"/> <expand macro="mod_option" value="Asn->Gln"/> <expand macro="mod_option" value="Asn->Glu"/> <expand macro="mod_option" value="Asn->Gly"/> <expand macro="mod_option" value="Asn->His"/> <expand macro="mod_option" value="Asn->Lys"/> <expand macro="mod_option" value="Asn->Met"/> <expand macro="mod_option" value="Asn->Phe"/> <expand macro="mod_option" value="Asn->Pro"/> <expand macro="mod_option" value="Asn->Ser"/> <expand macro="mod_option" value="Asn->Thr"/> <expand macro="mod_option" value="Asn->Trp"/> <expand macro="mod_option" value="Asn->Tyr"/> <expand macro="mod_option" value="Asn->Val"/> <expand macro="mod_option" value="Asn->Xle"/> <expand macro="mod_option" value="Asp->Ala"/> <expand macro="mod_option" value="Asp->Arg"/> <expand macro="mod_option" value="Asp->Asn"/> <expand macro="mod_option" value="Asp->Cys"/> <expand macro="mod_option" value="Asp->Gln"/> <expand macro="mod_option" value="Asp->Glu"/> <expand macro="mod_option" value="Asp->Gly"/> <expand macro="mod_option" value="Asp->His"/> <expand macro="mod_option" value="Asp->Lys"/> <expand macro="mod_option" value="Asp->Met"/> <expand macro="mod_option" value="Asp->Phe"/> <expand macro="mod_option" value="Asp->Pro"/> <expand macro="mod_option" value="Asp->Ser"/> <expand macro="mod_option" value="Asp->Thr"/> <expand macro="mod_option" value="Asp->Trp"/> <expand macro="mod_option" value="Asp->Tyr"/> <expand macro="mod_option" value="Asp->Val"/> <expand macro="mod_option" value="Asp->Xle"/> <expand macro="mod_option" value="Cys->Ala"/> <expand macro="mod_option" value="Cys->Arg"/> <expand macro="mod_option" value="Cys->Asn"/> <expand macro="mod_option" value="Cys->Asp"/> <expand macro="mod_option" value="Cys->Gln"/> <expand macro="mod_option" value="Cys->Glu"/> <expand macro="mod_option" value="Cys->Gly"/> <expand macro="mod_option" value="Cys->His"/> <expand macro="mod_option" value="Cys->Lys"/> <expand macro="mod_option" value="Cys->Met"/> <expand macro="mod_option" value="Cys->Phe"/> <expand macro="mod_option" value="Cys->Pro"/> <expand macro="mod_option" value="Cys->Ser"/> <expand macro="mod_option" value="Cys->Thr"/> <expand macro="mod_option" value="Cys->Trp"/> <expand macro="mod_option" value="Cys->Tyr"/> <expand macro="mod_option" value="Cys->Val"/> <expand macro="mod_option" value="Cys->Xle"/> <expand macro="mod_option" value="Gln->Ala"/> <expand macro="mod_option" value="Gln->Arg"/> <expand macro="mod_option" value="Gln->Asn"/> <expand macro="mod_option" value="Gln->Asp"/> <expand macro="mod_option" value="Gln->Cys"/> <expand macro="mod_option" value="Gln->Glu"/> <expand macro="mod_option" value="Gln->Gly"/> <expand macro="mod_option" value="Gln->His"/> <expand macro="mod_option" value="Gln->Lys"/> <expand macro="mod_option" value="Gln->Met"/> <expand macro="mod_option" value="Gln->Phe"/> <expand macro="mod_option" value="Gln->Pro"/> <expand macro="mod_option" value="Gln->Ser"/> <expand macro="mod_option" value="Gln->Thr"/> <expand macro="mod_option" value="Gln->Trp"/> <expand macro="mod_option" value="Gln->Tyr"/> <expand macro="mod_option" value="Gln->Val"/> <expand macro="mod_option" value="Gln->Xle"/> <expand macro="mod_option" value="Glu->Ala"/> <expand macro="mod_option" value="Glu->Arg"/> <expand macro="mod_option" value="Glu->Asn"/> <expand macro="mod_option" value="Glu->Asp"/> <expand macro="mod_option" value="Glu->Cys"/> <expand macro="mod_option" value="Glu->Gln"/> <expand macro="mod_option" value="Glu->Gly"/> <expand macro="mod_option" value="Glu->His"/> <expand macro="mod_option" value="Glu->Lys"/> <expand macro="mod_option" value="Glu->Met"/> <expand macro="mod_option" value="Glu->Phe"/> <expand macro="mod_option" value="Glu->Pro"/> <expand macro="mod_option" value="Glu->Ser"/> <expand macro="mod_option" value="Glu->Thr"/> <expand macro="mod_option" value="Glu->Trp"/> <expand macro="mod_option" value="Glu->Tyr"/> <expand macro="mod_option" value="Glu->Val"/> <expand macro="mod_option" value="Glu->Xle"/> <expand macro="mod_option" value="Gly->Ala"/> <expand macro="mod_option" value="Gly->Arg"/> <expand macro="mod_option" value="Gly->Asn"/> <expand macro="mod_option" value="Gly->Asp"/> <expand macro="mod_option" value="Gly->Cys"/> <expand macro="mod_option" value="Gly->Gln"/> <expand macro="mod_option" value="Gly->Glu"/> <expand macro="mod_option" value="Gly->His"/> <expand macro="mod_option" value="Gly->Lys"/> <expand macro="mod_option" value="Gly->Met"/> <expand macro="mod_option" value="Gly->Phe"/> <expand macro="mod_option" value="Gly->Pro"/> <expand macro="mod_option" value="Gly->Ser"/> <expand macro="mod_option" value="Gly->Thr"/> <expand macro="mod_option" value="Gly->Trp"/> <expand macro="mod_option" value="Gly->Tyr"/> <expand macro="mod_option" value="Gly->Val"/> <expand macro="mod_option" value="Gly->Xle"/> <expand macro="mod_option" value="His->Ala"/> <expand macro="mod_option" value="His->Arg"/> <expand macro="mod_option" value="His->Asn"/> <expand macro="mod_option" value="His->Asp"/> <expand macro="mod_option" value="His->Cys"/> <expand macro="mod_option" value="His->Gln"/> <expand macro="mod_option" value="His->Glu"/> <expand macro="mod_option" value="His->Gly"/> <expand macro="mod_option" value="His->Lys"/> <expand macro="mod_option" value="His->Met"/> <expand macro="mod_option" value="His->Phe"/> <expand macro="mod_option" value="His->Pro"/> <expand macro="mod_option" value="His->Ser"/> <expand macro="mod_option" value="His->Thr"/> <expand macro="mod_option" value="His->Trp"/> <expand macro="mod_option" value="His->Tyr"/> <expand macro="mod_option" value="His->Val"/> <expand macro="mod_option" value="His->Xle"/> <expand macro="mod_option" value="Lys->Ala"/> <expand macro="mod_option" value="Lys->Arg"/> <expand macro="mod_option" value="Lys->Asn"/> <expand macro="mod_option" value="Lys->Asp"/> <expand macro="mod_option" value="Lys->Cys"/> <expand macro="mod_option" value="Lys->Gln"/> <expand macro="mod_option" value="Lys->Glu"/> <expand macro="mod_option" value="Lys->Gly"/> <expand macro="mod_option" value="Lys->His"/> <expand macro="mod_option" value="Lys->Met"/> <expand macro="mod_option" value="Lys->Phe"/> <expand macro="mod_option" value="Lys->Pro"/> <expand macro="mod_option" value="Lys->Ser"/> <expand macro="mod_option" value="Lys->Thr"/> <expand macro="mod_option" value="Lys->Trp"/> <expand macro="mod_option" value="Lys->Tyr"/> <expand macro="mod_option" value="Lys->Val"/> <expand macro="mod_option" value="Lys->Xle"/> <expand macro="mod_option" value="Met->Ala"/> <expand macro="mod_option" value="Met->Arg"/> <expand macro="mod_option" value="Met->Asn"/> <expand macro="mod_option" value="Met->Asp"/> <expand macro="mod_option" value="Met->Cys"/> <expand macro="mod_option" value="Met->Gln"/> <expand macro="mod_option" value="Met->Glu"/> <expand macro="mod_option" value="Met->Gly"/> <expand macro="mod_option" value="Met->His"/> <expand macro="mod_option" value="Met->Lys"/> <expand macro="mod_option" value="Met->Phe"/> <expand macro="mod_option" value="Met->Pro"/> <expand macro="mod_option" value="Met->Ser"/> <expand macro="mod_option" value="Met->Thr"/> <expand macro="mod_option" value="Met->Trp"/> <expand macro="mod_option" value="Met->Tyr"/> <expand macro="mod_option" value="Met->Val"/> <expand macro="mod_option" value="Met->Xle"/> <expand macro="mod_option" value="Phe->Ala"/> <expand macro="mod_option" value="Phe->Arg"/> <expand macro="mod_option" value="Phe->Asn"/> <expand macro="mod_option" value="Phe->Asp"/> <expand macro="mod_option" value="Phe->Cys"/> <expand macro="mod_option" value="Phe->Gln"/> <expand macro="mod_option" value="Phe->Glu"/> <expand macro="mod_option" value="Phe->Gly"/> <expand macro="mod_option" value="Phe->His"/> <expand macro="mod_option" value="Phe->Lys"/> <expand macro="mod_option" value="Phe->Met"/> <expand macro="mod_option" value="Phe->Pro"/> <expand macro="mod_option" value="Phe->Ser"/> <expand macro="mod_option" value="Phe->Thr"/> <expand macro="mod_option" value="Phe->Trp"/> <expand macro="mod_option" value="Phe->Tyr"/> <expand macro="mod_option" value="Phe->Val"/> <expand macro="mod_option" value="Phe->Xle"/> <expand macro="mod_option" value="Pro->Ala"/> <expand macro="mod_option" value="Pro->Arg"/> <expand macro="mod_option" value="Pro->Asn"/> <expand macro="mod_option" value="Pro->Asp"/> <expand macro="mod_option" value="Pro->Cys"/> <expand macro="mod_option" value="Pro->Gln"/> <expand macro="mod_option" value="Pro->Glu"/> <expand macro="mod_option" value="Pro->Gly"/> <expand macro="mod_option" value="Pro->His"/> <expand macro="mod_option" value="Pro->Lys"/> <expand macro="mod_option" value="Pro->Met"/> <expand macro="mod_option" value="Pro->Phe"/> <expand macro="mod_option" value="Pro->Ser"/> <expand macro="mod_option" value="Pro->Thr"/> <expand macro="mod_option" value="Pro->Trp"/> <expand macro="mod_option" value="Pro->Tyr"/> <expand macro="mod_option" value="Pro->Val"/> <expand macro="mod_option" value="Pro->Xle"/> <expand macro="mod_option" value="Ser->Ala"/> <expand macro="mod_option" value="Ser->Arg"/> <expand macro="mod_option" value="Ser->Asn"/> <expand macro="mod_option" value="Ser->Asp"/> <expand macro="mod_option" value="Ser->Cys"/> <expand macro="mod_option" value="Ser->Gln"/> <expand macro="mod_option" value="Ser->Glu"/> <expand macro="mod_option" value="Ser->Gly"/> <expand macro="mod_option" value="Ser->His"/> <expand macro="mod_option" value="Ser->Lys"/> <expand macro="mod_option" value="Ser->Met"/> <expand macro="mod_option" value="Ser->Phe"/> <expand macro="mod_option" value="Ser->Pro"/> <expand macro="mod_option" value="Ser->Thr"/> <expand macro="mod_option" value="Ser->Trp"/> <expand macro="mod_option" value="Ser->Tyr"/> <expand macro="mod_option" value="Ser->Val"/> <expand macro="mod_option" value="Ser->Xle"/> <expand macro="mod_option" value="Thr->Ala"/> <expand macro="mod_option" value="Thr->Arg"/> <expand macro="mod_option" value="Thr->Asn"/> <expand macro="mod_option" value="Thr->Asp"/> <expand macro="mod_option" value="Thr->Cys"/> <expand macro="mod_option" value="Thr->Gln"/> <expand macro="mod_option" value="Thr->Glu"/> <expand macro="mod_option" value="Thr->Gly"/> <expand macro="mod_option" value="Thr->His"/> <expand macro="mod_option" value="Thr->Lys"/> <expand macro="mod_option" value="Thr->Met"/> <expand macro="mod_option" value="Thr->Phe"/> <expand macro="mod_option" value="Thr->Pro"/> <expand macro="mod_option" value="Thr->Ser"/> <expand macro="mod_option" value="Thr->Trp"/> <expand macro="mod_option" value="Thr->Tyr"/> <expand macro="mod_option" value="Thr->Val"/> <expand macro="mod_option" value="Thr->Xle"/> <expand macro="mod_option" value="Trp->Ala"/> <expand macro="mod_option" value="Trp->Arg"/> <expand macro="mod_option" value="Trp->Asn"/> <expand macro="mod_option" value="Trp->Asp"/> <expand macro="mod_option" value="Trp->Cys"/> <expand macro="mod_option" value="Trp->Gln"/> <expand macro="mod_option" value="Trp->Glu"/> <expand macro="mod_option" value="Trp->Gly"/> <expand macro="mod_option" value="Trp->His"/> <expand macro="mod_option" value="Trp->Lys"/> <expand macro="mod_option" value="Trp->Met"/> <expand macro="mod_option" value="Trp->Phe"/> <expand macro="mod_option" value="Trp->Pro"/> <expand macro="mod_option" value="Trp->Ser"/> <expand macro="mod_option" value="Trp->Thr"/> <expand macro="mod_option" value="Trp->Tyr"/> <expand macro="mod_option" value="Trp->Val"/> <expand macro="mod_option" value="Trp->Xle"/> <expand macro="mod_option" value="Tyr->Ala"/> <expand macro="mod_option" value="Tyr->Arg"/> <expand macro="mod_option" value="Tyr->Asn"/> <expand macro="mod_option" value="Tyr->Asp"/> <expand macro="mod_option" value="Tyr->Cys"/> <expand macro="mod_option" value="Tyr->Gln"/> <expand macro="mod_option" value="Tyr->Glu"/> <expand macro="mod_option" value="Tyr->Gly"/> <expand macro="mod_option" value="Tyr->His"/> <expand macro="mod_option" value="Tyr->Lys"/> <expand macro="mod_option" value="Tyr->Met"/> <expand macro="mod_option" value="Tyr->Phe"/> <expand macro="mod_option" value="Tyr->Pro"/> <expand macro="mod_option" value="Tyr->Ser"/> <expand macro="mod_option" value="Tyr->Thr"/> <expand macro="mod_option" value="Tyr->Trp"/> <expand macro="mod_option" value="Tyr->Val"/> <expand macro="mod_option" value="Tyr->Xle"/> <expand macro="mod_option" value="Val->Ala"/> <expand macro="mod_option" value="Val->Arg"/> <expand macro="mod_option" value="Val->Asn"/> <expand macro="mod_option" value="Val->Asp"/> <expand macro="mod_option" value="Val->Cys"/> <expand macro="mod_option" value="Val->Gln"/> <expand macro="mod_option" value="Val->Glu"/> <expand macro="mod_option" value="Val->Gly"/> <expand macro="mod_option" value="Val->His"/> <expand macro="mod_option" value="Val->Lys"/> <expand macro="mod_option" value="Val->Met"/> <expand macro="mod_option" value="Val->Phe"/> <expand macro="mod_option" value="Val->Pro"/> <expand macro="mod_option" value="Val->Ser"/> <expand macro="mod_option" value="Val->Thr"/> <expand macro="mod_option" value="Val->Trp"/> <expand macro="mod_option" value="Val->Tyr"/> <expand macro="mod_option" value="Val->Xle"/> <expand macro="mod_option" value="Xle->Ala"/> <expand macro="mod_option" value="Xle->Arg"/> <expand macro="mod_option" value="Xle->Asn"/> <expand macro="mod_option" value="Xle->Asp"/> <expand macro="mod_option" value="Xle->Cys"/> <expand macro="mod_option" value="Xle->Gln"/> <expand macro="mod_option" value="Xle->Glu"/> <expand macro="mod_option" value="Xle->Gly"/> <expand macro="mod_option" value="Xle->His"/> <expand macro="mod_option" value="Xle->Lys"/> <expand macro="mod_option" value="Xle->Met"/> <expand macro="mod_option" value="Xle->Phe"/> <expand macro="mod_option" value="Xle->Pro"/> <expand macro="mod_option" value="Xle->Ser"/> <expand macro="mod_option" value="Xle->Thr"/> <expand macro="mod_option" value="Xle->Trp"/> <expand macro="mod_option" value="Xle->Tyr"/> <expand macro="mod_option" value="Xle->Val"/> <expand macro="mod_option" value="CamCys->Ala"/> <expand macro="mod_option" value="CamCys->Arg"/> <expand macro="mod_option" value="CamCys->Asn"/> <expand macro="mod_option" value="CamCys->Asp"/> <expand macro="mod_option" value="CamCys->Gln"/> <expand macro="mod_option" value="CamCys->Glu"/> <expand macro="mod_option" value="CamCys->Gly"/> <expand macro="mod_option" value="CamCys->His"/> <expand macro="mod_option" value="CamCys->Lys"/> <expand macro="mod_option" value="CamCys->Met"/> <expand macro="mod_option" value="CamCys->Phe"/> <expand macro="mod_option" value="CamCys->Pro"/> <expand macro="mod_option" value="CamCys->Ser"/> <expand macro="mod_option" value="CamCys->Thr"/> <expand macro="mod_option" value="CamCys->Trp"/> <expand macro="mod_option" value="CamCys->Tyr"/> <expand macro="mod_option" value="CamCys->Val"/> <expand macro="mod_option" value="CamCys->Xle"/> <expand macro="mod_option" value="Ala->CamCys"/> <expand macro="mod_option" value="Arg->CamCys"/> <expand macro="mod_option" value="Asn->CamCys"/> <expand macro="mod_option" value="Asp->CamCys"/> <expand macro="mod_option" value="Gln->CamCys"/> <expand macro="mod_option" value="Glu->CamCys"/> <expand macro="mod_option" value="Gly->CamCys"/> <expand macro="mod_option" value="His->CamCys"/> <expand macro="mod_option" value="Lys->CamCys"/> <expand macro="mod_option" value="Met->CamCys"/> <expand macro="mod_option" value="Phe->CamCys"/> <expand macro="mod_option" value="Pro->CamCys"/> <expand macro="mod_option" value="Ser->CamCys"/> <expand macro="mod_option" value="Thr->CamCys"/> <expand macro="mod_option" value="Trp->CamCys"/> <expand macro="mod_option" value="Tyr->CamCys"/> <expand macro="mod_option" value="Val->CamCys"/> <expand macro="mod_option" value="Xle->CamCys"/> <expand macro="mod_option" value="Cysteinyl"/> <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/> <expand macro="mod_option" value="Oxidation (MP)"/> <expand macro="mod_option" value="Propionamide (C)"/> <expand macro="mod_option" value="Propionamide (K)"/> <expand macro="mod_option" value="Propionamide (N-term)"/> <expand macro="mod_option" value="PhosphoGlyceroyl-Lys (K)"/> <expand macro="mod_option" value="Glyceroyl-Lys (K)"/> <expand macro="mod_option" value="Propionyl (K)"/> </xml> <xml name="label"> <expand macro="mod_option" value="Arg6"/> <expand macro="mod_option" value="Arg10"/> <expand macro="mod_option" value="Lys4"/> <expand macro="mod_option" value="Lys6"/> <expand macro="mod_option" value="Lys8"/> <expand macro="mod_option" value="DimethLys0"/> <expand macro="mod_option" value="DimethNter0"/> <expand macro="mod_option" value="DimethLys4"/> <expand macro="mod_option" value="DimethNter4"/> <expand macro="mod_option" value="DimethLys8"/> <expand macro="mod_option" value="DimethNter8"/> <expand macro="mod_option" value="18O"/> <expand macro="mod_option" value="ICAT-0"/> <expand macro="mod_option" value="ICAT-9"/> <expand macro="mod_option" value="ICPL-Lys0"/> <expand macro="mod_option" value="ICPL-Nter0"/> <expand macro="mod_option" value="ICPL-Lys4"/> <expand macro="mod_option" value="ICPL-Nter4"/> <expand macro="mod_option" value="ICPL-Lys6"/> <expand macro="mod_option" value="ICPL-Nter6"/> <expand macro="mod_option" value="ICPL-Lys10"/> <expand macro="mod_option" value="ICPL-Nter10"/> <expand macro="mod_option" value="mTRAQ-Lys0"/> <expand macro="mod_option" value="mTRAQ-Nter0"/> <expand macro="mod_option" value="mTRAQ-Lys4"/> <expand macro="mod_option" value="mTRAQ-Nter4"/> <expand macro="mod_option" value="mTRAQ-Lys8"/> <expand macro="mod_option" value="mTRAQ-Nter8"/> <expand macro="mod_option" value="DimethLys2"/> <expand macro="mod_option" value="DimethNter2"/> <expand macro="mod_option" value="DimethLys6"/> <expand macro="mod_option" value="DimethNter6"/> <expand macro="mod_option" value="Leu7"/> <expand macro="mod_option" value="Ile7"/> </xml> <xml name="proteases"> <expand macro="mod_option" value="Trypsin"/> <expand macro="mod_option" value="LysC"/> <expand macro="mod_option" value="LysC/P"/> <expand macro="mod_option" value="D.P"/> <expand macro="mod_option" value="ArgC"/> <expand macro="mod_option" value="AspC"/> <expand macro="mod_option" value="GluC"/> <expand macro="mod_option" value="GluN"/> <expand macro="mod_option" value="AspN"/> <expand macro="mod_option" value="LysN"/> <expand macro="mod_option" value="Chymotrypsin+"/> <expand macro="mod_option" value="Chymotrypsin"/> </xml> <xml name="iso_labels"> <expand macro="mod_option" value="iTRAQ4plex-Nter114"/> <expand macro="mod_option" value="iTRAQ4plex-Nter115"/> <expand macro="mod_option" value="iTRAQ4plex-Nter116"/> <expand macro="mod_option" value="iTRAQ4plex-Nter117"/> <expand macro="mod_option" value="iTRAQ4plex-Lys114"/> <expand macro="mod_option" value="iTRAQ4plex-Lys115"/> <expand macro="mod_option" value="iTRAQ4plex-Lys116"/> <expand macro="mod_option" value="iTRAQ4plex-Lys117"/> <expand macro="mod_option" value="iTRAQ8plex-Nter113"/> <expand macro="mod_option" value="iTRAQ8plex-Nter114"/> <expand macro="mod_option" value="iTRAQ8plex-Nter115"/> <expand macro="mod_option" value="iTRAQ8plex-Nter116"/> <expand macro="mod_option" value="iTRAQ8plex-Nter117"/> <expand macro="mod_option" value="iTRAQ8plex-Nter118"/> <expand macro="mod_option" value="iTRAQ8plex-Nter119"/> <expand macro="mod_option" value="iTRAQ8plex-Nter121"/> <expand macro="mod_option" value="iTRAQ8plex-Lys113"/> <expand macro="mod_option" value="iTRAQ8plex-Lys114"/> <expand macro="mod_option" value="iTRAQ8plex-Lys115"/> <expand macro="mod_option" value="iTRAQ8plex-Lys116"/> <expand macro="mod_option" value="iTRAQ8plex-Lys117"/> <expand macro="mod_option" value="iTRAQ8plex-Lys118"/> <expand macro="mod_option" value="iTRAQ8plex-Lys119"/> <expand macro="mod_option" value="iTRAQ8plex-Lys121"/> <expand macro="mod_option" value="TMT2plex-Nter126"/> <expand macro="mod_option" value="TMT2plex-Nter127"/> <expand macro="mod_option" value="TMT2plex-Lys126"/> <expand macro="mod_option" value="TMT2plex-Lys127"/> <expand macro="mod_option" value="TMT6plex-Nter126"/> <expand macro="mod_option" value="TMT6plex-Nter127"/> <expand macro="mod_option" value="TMT6plex-Nter128"/> <expand macro="mod_option" value="TMT6plex-Nter129"/> <expand macro="mod_option" value="TMT6plex-Nter130"/> <expand macro="mod_option" value="TMT6plex-Nter131"/> <expand macro="mod_option" value="TMT8plex-Nter126C"/> <expand macro="mod_option" value="TMT8plex-Nter127N"/> <expand macro="mod_option" value="TMT8plex-Nter127C"/> <expand macro="mod_option" value="TMT8plex-Nter128C"/> <expand macro="mod_option" value="TMT8plex-Nter129N"/> <expand macro="mod_option" value="TMT8plex-Nter129C"/> <expand macro="mod_option" value="TMT8plex-Nter130C"/> <expand macro="mod_option" value="TMT8plex-Nter131N"/> <expand macro="mod_option" value="TMT10plex-Nter126C"/> <expand macro="mod_option" value="TMT10plex-Nter127N"/> <expand macro="mod_option" value="TMT10plex-Nter127C"/> <expand macro="mod_option" value="TMT10plex-Nter128N"/> <expand macro="mod_option" value="TMT10plex-Nter128C"/> <expand macro="mod_option" value="TMT10plex-Nter129N"/> <expand macro="mod_option" value="TMT10plex-Nter129C"/> <expand macro="mod_option" value="TMT10plex-Nter130N"/> <expand macro="mod_option" value="TMT10plex-Nter130C"/> <expand macro="mod_option" value="TMT10plex-Nter131N"/> <expand macro="mod_option" value="TMT11plex-Nter131C"/> <expand macro="mod_option" value="TMT6plex-Lys126"/> <expand macro="mod_option" value="TMT6plex-Lys127"/> <expand macro="mod_option" value="TMT6plex-Lys128"/> <expand macro="mod_option" value="TMT6plex-Lys129"/> <expand macro="mod_option" value="TMT6plex-Lys130"/> <expand macro="mod_option" value="TMT6plex-Lys131"/> <expand macro="mod_option" value="TMT8plex-Lys126C"/> <expand macro="mod_option" value="TMT8plex-Lys127N"/> <expand macro="mod_option" value="TMT8plex-Lys127C"/> <expand macro="mod_option" value="TMT8plex-Lys128C"/> <expand macro="mod_option" value="TMT8plex-Lys129N"/> <expand macro="mod_option" value="TMT8plex-Lys129C"/> <expand macro="mod_option" value="TMT8plex-Lys130C"/> <expand macro="mod_option" value="TMT8plex-Lys131N"/> <expand macro="mod_option" value="TMT10plex-Lys126C"/> <expand macro="mod_option" value="TMT10plex-Lys127N"/> <expand macro="mod_option" value="TMT10plex-Lys127C"/> <expand macro="mod_option" value="TMT10plex-Lys128N"/> <expand macro="mod_option" value="TMT10plex-Lys128C"/> <expand macro="mod_option" value="TMT10plex-Lys129N"/> <expand macro="mod_option" value="TMT10plex-Lys129C"/> <expand macro="mod_option" value="TMT10plex-Lys130N"/> <expand macro="mod_option" value="TMT10plex-Lys130C"/> <expand macro="mod_option" value="TMT10plex-Lys131N"/> <expand macro="mod_option" value="TMT11plex-Lys131C"/> <expand macro="mod_option" value="iodoTMT6plex-Cys126"/> <expand macro="mod_option" value="iodoTMT6plex-Cys127"/> <expand macro="mod_option" value="iodoTMT6plex-Cys128"/> <expand macro="mod_option" value="iodoTMT6plex-Cys129"/> <expand macro="mod_option" value="iodoTMT6plex-Cys130"/> <expand macro="mod_option" value="iodoTMT6plex-Cys131"/> <expand macro="mod_option" value="TMTpro16plex-Nter126C"/> <expand macro="mod_option" value="TMTpro16plex-Nter127N"/> <expand macro="mod_option" value="TMTpro16plex-Nter127C"/> <expand macro="mod_option" value="TMTpro16plex-Nter128N"/> <expand macro="mod_option" value="TMTpro16plex-Nter128C"/> <expand macro="mod_option" value="TMTpro16plex-Nter129N"/> <expand macro="mod_option" value="TMTpro16plex-Nter129C"/> <expand macro="mod_option" value="TMTpro16plex-Nter130N"/> <expand macro="mod_option" value="TMTpro16plex-Nter130C"/> <expand macro="mod_option" value="TMTpro16plex-Nter131N"/> <expand macro="mod_option" value="TMTpro16plex-Nter131C"/> <expand macro="mod_option" value="TMTpro16plex-Nter132N"/> <expand macro="mod_option" value="TMTpro16plex-Nter132C"/> <expand macro="mod_option" value="TMTpro16plex-Nter133N"/> <expand macro="mod_option" value="TMTpro16plex-Nter133C"/> <expand macro="mod_option" value="TMTpro16plex-Nter134N"/> <expand macro="mod_option" value="TMTpro16plex-Lys126C"/> <expand macro="mod_option" value="TMTpro16plex-Lys127N"/> <expand macro="mod_option" value="TMTpro16plex-Lys127C"/> <expand macro="mod_option" value="TMTpro16plex-Lys128N"/> <expand macro="mod_option" value="TMTpro16plex-Lys128C"/> <expand macro="mod_option" value="TMTpro16plex-Lys129N"/> <expand macro="mod_option" value="TMTpro16plex-Lys129C"/> <expand macro="mod_option" value="TMTpro16plex-Lys130N"/> <expand macro="mod_option" value="TMTpro16plex-Lys130C"/> <expand macro="mod_option" value="TMTpro16plex-Lys131N"/> <expand macro="mod_option" value="TMTpro16plex-Lys131C"/> <expand macro="mod_option" value="TMTpro16plex-Lys132N"/> <expand macro="mod_option" value="TMTpro16plex-Lys132C"/> <expand macro="mod_option" value="TMTpro16plex-Lys133N"/> <expand macro="mod_option" value="TMTpro16plex-Lys133C"/> <expand macro="mod_option" value="TMTpro16plex-Lys134N"/> <expand macro="mod_option" value="TMTpro18plex-Nter134C"/> <expand macro="mod_option" value="TMTpro18plex-Nter135N"/> <expand macro="mod_option" value="TMTpro18plex-Lys134C"/> <expand macro="mod_option" value="TMTpro18plex-Lys135N"/> </xml> <xml name="reporter_ion_macro"> <conditional name="iso_labels"> <param name="labeling" type="select" label="isobaric labeling" help="Select one of the standard labelings (correction factors are zero) or create a custom labeling."> <option value="custom">custom</option> <option value="tmt2plex">TMT2plex</option> <option value="tmt6plex">TMT6plex</option> <option value="tmt8plex">TMT8plex</option> <option value="tmt10plex">TMT10plex</option> <option value="tmt11plex">TMT11plex</option> <option value="tmtpro16plex">TMTpro16plex</option> <option value="tmtpro18plex">TMTpro18plex</option> <option value="itraq4plex">iTRAQ4plex</option> <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> </param> <when value="tmt2plex"/> <when value="tmt6plex"/> <when value="tmt8plex"/> <when value="tmt10plex"/> <when value="tmt11plex"/> <when value="tmtpro16plex"/> <when value="tmtpro18plex"/> <when value="itraq4plex"/> <when value="itraq8plex"/> <when value="iodotmt6plex"/> <when value="custom"> <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> <param name="internallabel" type="select" label="internal label" help="contains Lys"> <expand macro="iso_labels"/> </param> <param name="terminallabel" type="select" label="terminal label" help="contains Nter"> <option value="">None</option> <expand macro="iso_labels"/> </param> <param name="cm2" type="float" label="correction factor -2%" value="0.0"/> <param name="cm1" type="float" label="correction factor -1%" value="0.0"/> <param name="cp1" type="float" label="correction factor +1%" value="0.0"/> <param name="cp2" type="float" label="correction factor +2%" value="0.0"/> <param type="boolean" name="tmtlike" checked="false" label="TMT-like" truevalue="true" falsevalue="false"/> </repeat> </when> </conditional> <conditional name="filter_by_pif"> <param name="filter_pif" type="select" label="Filter by PIF" help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."> <option value="True">True</option> <option value="False" selected="true">False</option> </param> <when value="True"> <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" max="1" help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> </when> <when value="False"/> </conditional> </xml> <xml name="citations"> <citations> <citation type="bibtex"> @article{cox2008maxquant, title={MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification}, author={Cox, J{\"u}rgen and Mann, Matthias}, journal={Nature biotechnology}, volume={26}, number={12}, pages={1367}, year={2008}, publisher={Nature Publishing Group} } </citation> <citation type="bibtex"> @article{tyanova2016maxquant, title={The MaxQuant computational platform for mass spectrometry-based shotgun proteomics}, author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen}, journal={Nature protocols}, volume={11}, number={12}, pages={2301}, year={2016}, publisher={Nature Publishing Group} } </citation> <citation type="doi">10.1021/acs.jproteome.5b00780</citation> <citation type="doi">10.1021/acs.jproteome.2c00051</citation> </citations> </xml> </macros>