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Add the module to convert DIA-NN output to msstats.csv.
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@fcyu
fcyu committed Jul 2, 2023
1 parent 1b1dbf6 commit 4a3d0d3
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Showing 124 changed files with 452 additions and 3 deletions.
1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/DIA_DIA-Umpire_SpecLib_Quant.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/DIA_SpecLib_Quant.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Default.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Diagnostic-ion-mining.workflow
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crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/FPOP.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/LFQ-MBR.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/LFQ-phospho.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/LFQ-ubiquitin.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Labile_ADP-ribosylation.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Labile_phospho.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Mass-Offset-CommonPTMs.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Nonspecific-HLA-C57.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Nonspecific-HLA-DIA.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Nonspecific-HLA-TMT10.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Nonspecific-HLA-glyco.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Nonspecific-HLA-phospho.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Nonspecific-HLA.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Nonspecific-peptidome.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Open-quickscan.workflow
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crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/Open.workflow
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crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/SILAC3-phospho.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/SILAC3.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/SLC-ABPP.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-MS3-phospho.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-MS3.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-Open.workflow
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crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-acetyl-noloc.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-acetyl.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-bridge.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-phospho-bridge.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-phospho.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-ubiquitin.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-ubiquitination-K_tmt_or_ubiq.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10-ubiquitination-K_tmt_plus_ubiq.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT10.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT16-MS3.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT16-acetyl-noloc.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT16-acetyl.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT16-phospho.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/TMT16.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/XRNAX-MassOffset.workflow
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crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/diaTOP_ABPP.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/glyco-N-HCD.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/glyco-N-Hybrid.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/glyco-N-LFQ.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/glyco-N-TMT.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/glyco-N-open-HCD.workflow
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crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/glyco-N-open-Hybrid.workflow
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crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/glyco-O-HCD.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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1 change: 1 addition & 0 deletions MSFragger-GUI/resources/workflows/glyco-O-Hybrid.workflow
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crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=false
diann.heavy=
diann.library=
diann.light=
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