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Further revise comments in example parameter files
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@alchemistmatt
alchemistmatt committed Sep 15, 2022
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_ProOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
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Expand Up @@ -23,8 +23,8 @@ DynamicMod=O1, MP, opt, any, Oxidation # Oxidized methionine and prol
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_CustomAA_O_Hydroxyproline_20ppmParTol.txt
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Expand Up @@ -24,8 +24,8 @@ CustomAA=C5H7N1O2S0, O, custom, P, Hydroxylation # Hydroxyproline
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions ...ameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_NTermAcet_NQR_Deamide_Stat_CysAlk_20ppmParTol.txt
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Expand Up @@ -23,8 +23,8 @@ DynamicMod=H-1N-1O1, NQR, opt, any, Deamidated # Deamidation of Gluta
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionin
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ DynamicMod=None
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ DynamicMod=none
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_Tryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_Tryp_DynSTYPhos_Stat_CysAlk_TMT_6Plex_Protocol1_20ppmParTol.txt
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Expand Up @@ -23,8 +23,8 @@ DynamicMod=HO3P, STY, opt, any, Phospho # Phosphorylati
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_Tryp_Dyn_MetOx_STYPhos_Stat_CysAlk_20ppmParTol.txt
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Expand Up @@ -22,8 +22,8 @@ DynamicMod=HO3P, STY, opt, any, Phospho # Phosphorylation
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_Tryp_MetOx_15ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_Tryp_MetOx_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=0
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_Tryp_MetOx_StatCysAlk_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionin
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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4 changes: 2 additions & 2 deletions docs/ParameterFiles/MSGFPlus_Tryp_NoMods_20ppmParTol.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ DynamicMod=None
FragmentationMethodID=0

# Instrument ID
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra
# 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra
# 2 means TOF
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
InstrumentID=1
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