Skip to content

Commit 2712ab0

Browse files
alchemistmattalchemistmatt
committed
Further revise comments in example parameter files
1 parent 9887d10 commit 2712ab0

17 files changed

+34
-34
lines changed

‎docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_ProOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,8 @@ DynamicMod=O1, MP, opt, any, Oxidation # Oxidized methionine and prol
2323
FragmentationMethodID=0
2424

2525
# Instrument ID
26-
# 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
27-
# 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
26+
# 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
27+
# 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
2828
# 2 means TOF
2929
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
3030
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth
2323
FragmentationMethodID=0
2424

2525
# Instrument ID
26-
# 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
27-
# 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
26+
# 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
27+
# 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
2828
# 2 means TOF
2929
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
3030
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine
2323
FragmentationMethodID=0
2424

2525
# Instrument ID
26-
# 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
27-
# 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
26+
# 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
27+
# 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
2828
# 2 means TOF
2929
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
3030
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -22,8 +22,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth
2222
FragmentationMethodID=0
2323

2424
# Instrument ID
25-
# 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
26-
# 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
25+
# 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
26+
# 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
2727
# 2 means TOF
2828
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
2929
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_CustomAA_O_Hydroxyproline_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -24,8 +24,8 @@ CustomAA=C5H7N1O2S0, O, custom, P, Hydroxylation # Hydroxyproline
2424
FragmentationMethodID=0
2525

2626
# Instrument ID
27-
# 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
28-
# 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
27+
# 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
28+
# 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
2929
# 2 means TOF
3030
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
3131
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_NTermAcet_NQR_Deamide_Stat_CysAlk_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,8 @@ DynamicMod=H-1N-1O1, NQR, opt, any, Deamidated # Deamidation of Gluta
2323
FragmentationMethodID=0
2424

2525
# Instrument ID
26-
# 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
27-
# 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
26+
# 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
27+
# 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
2828
# 2 means TOF
2929
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
3030
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,8 +21,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine
2121
FragmentationMethodID=0
2222

2323
# Instrument ID
24-
# 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
25-
# 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
24+
# 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
25+
# 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
2626
# 2 means TOF
2727
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
2828
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,8 +21,8 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionin
2121
FragmentationMethodID=0
2222

2323
# Instrument ID
24-
# 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
25-
# 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
24+
# 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
25+
# 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
2626
# 2 means TOF
2727
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
2828
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,8 +21,8 @@ DynamicMod=None
2121
FragmentationMethodID=0
2222

2323
# Instrument ID
24-
# 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
25-
# 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
24+
# 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
25+
# 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
2626
# 2 means TOF
2727
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
2828
InstrumentID=1

‎docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,8 @@ DynamicMod=none
2323
FragmentationMethodID=0
2424

2525
# Instrument ID
26-
# 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
27-
# 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
26+
# 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
27+
# 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
2828
# 2 means TOF
2929
# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
3030
InstrumentID=1

0 commit comments

Comments
 (0)