Update comments in MS-GF+ parameter files

MSGFPlus · Sep 7, 2021 · f846ded · f846ded
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diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_ProOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_ProOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
@@ -19,7 +19,7 @@ DynamicMod=O1, MP, opt, any, Oxidation            # Oxidized methionine and prol
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID

diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
@@ -1,9 +1,9 @@
-# Parent mass tolerance 
+# Precursor mass tolerance
 #  Examples: 2.5Da or 30ppm
 #  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
 PrecursorMassTolerance=20ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Dynamic (Variable) Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -19,7 +19,7 @@ DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized meth
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID
@@ -77,6 +77,24 @@ MaxCharge=5
 # If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
 NumMatchesPerSpec=1
 
+# Mass of charge carrier
+#  Default: mass of proton
+#ChargeCarrierMass=1.00727649
+
+# Maximum missed cleavages
+#  Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
+#MaxMissedCleavages=-1
+
+# Minimum number of ions a spectrum must have to be examined
+#MinNumPeaksPerSpectrum=10
+
+# Number of isoforms to consider per peptide
+#  Default: 128
+#NumIsoforms=128
+
+# Include additional features in the output (enable this to post-process results with Percolator)
+#AddFeatures=1
+
 # Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries

diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt
@@ -19,7 +19,7 @@ DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID

diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt
@@ -1,9 +1,9 @@
-# Parent mass tolerance 
+# Precursor mass tolerance
 #  Examples: 2.5Da or 30ppm
 #  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
 PrecursorMassTolerance=20ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Dynamic (Variable) Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -18,7 +18,7 @@ DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized meth
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID
@@ -76,6 +76,24 @@ MaxCharge=5
 # If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
 NumMatchesPerSpec=1
 
+# Mass of charge carrier
+#  Default: mass of proton
+#ChargeCarrierMass=1.00727649
+
+# Maximum missed cleavages
+#  Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
+#MaxMissedCleavages=-1
+
+# Minimum number of ions a spectrum must have to be examined
+#MinNumPeaksPerSpectrum=10
+
+# Number of isoforms to consider per peptide
+#  Default: 128
+#NumIsoforms=128
+
+# Include additional features in the output (enable this to post-process results with Percolator)
+#AddFeatures=1
+
 # Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries

diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_CustomAA_O_Hydroxyproline_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_CustomAA_O_Hydroxyproline_20ppmParTol.txt
@@ -20,7 +20,7 @@ CustomAA=C5H7N1O2S0,   O,  custom, P, Hydroxylation     # Hydroxyproline
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID

diff --git a/...ameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_NTermAcet_NQR_Deamide_Stat_CysAlk_20ppmParTol.txt b/...ameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_NTermAcet_NQR_Deamide_Stat_CysAlk_20ppmParTol.txt
@@ -3,7 +3,7 @@
 #  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
 PrecursorMassTolerance=20ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Dynamic (Variable) Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -19,7 +19,7 @@ DynamicMod=H-1N-1O1, NQR, opt, any, Deamidated           	# Deamidation of Gluta
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
 FragmentationMethodID=0
 
 # Instrument ID
@@ -77,6 +77,24 @@ MaxCharge=5
 # If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
 NumMatchesPerSpec=1
 
+# Mass of charge carrier
+#  Default: mass of proton
+#ChargeCarrierMass=1.00727649
+
+# Maximum missed cleavages
+#  Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
+#MaxMissedCleavages=-1
+
+# Minimum number of ions a spectrum must have to be examined
+#MinNumPeaksPerSpectrum=10
+
+# Number of isoforms to consider per peptide
+#  Default: 128
+#NumIsoforms=128
+
+# Include additional features in the output (enable this to post-process results with Percolator)
+#AddFeatures=1
+
 # Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries

diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt
@@ -1,9 +1,9 @@
-# Parent mass tolerance 
+# Precursor mass tolerance
 #  Examples: 2.5Da or 30ppm
 #  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
 PrecursorMassTolerance=20ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Dynamic (Variable) Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -74,6 +74,24 @@ MaxCharge=5
 # If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
 NumMatchesPerSpec=1
 
+# Mass of charge carrier
+#  Default: mass of proton
+#ChargeCarrierMass=1.00727649
+
+# Maximum missed cleavages
+#  Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
+#MaxMissedCleavages=-1
+
+# Minimum number of ions a spectrum must have to be examined
+#MinNumPeaksPerSpectrum=10
+
+# Number of isoforms to consider per peptide
+#  Default: 128
+#NumIsoforms=128
+
+# Include additional features in the output (enable this to post-process results with Percolator)
+#AddFeatures=1
+
 # Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries

diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt
@@ -1,9 +1,9 @@
-# Parent mass tolerance 
+# Precursor mass tolerance
 #  Examples: 2.5Da or 30ppm
 #  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
 PrecursorMassTolerance=20ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Dynamic (Variable) Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -17,7 +17,7 @@ DynamicMod=O1,       M, opt, any, Oxidation                 # Oxidized methionin
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID
@@ -75,6 +75,24 @@ MaxCharge=5
 # If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
 NumMatchesPerSpec=1
 
+# Mass of charge carrier
+#  Default: mass of proton
+#ChargeCarrierMass=1.00727649
+
+# Maximum missed cleavages
+#  Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
+#MaxMissedCleavages=-1
+
+# Minimum number of ions a spectrum must have to be examined
+MinNumPeaksPerSpectrum=5
+
+# Number of isoforms to consider per peptide
+#  Default: 128
+#NumIsoforms=128
+
+# Include additional features in the output (enable this to post-process results with Percolator)
+AddFeatures=1
+
 # Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries

diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt
@@ -1,9 +1,9 @@
-# Parent mass tolerance 
+# Precursor mass tolerance
 #  Examples: 2.5Da or 30ppm
 #  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
 PrecursorMassTolerance=20ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Dynamic (Variable) Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -17,7 +17,8 @@ DynamicMod=None
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
+# (note that for Thermo instruments this is always set to 0 by the Analysis Manager since a _ScanType.txt file is created with this information on a per-scan basis)
 FragmentationMethodID=0
 
 # Instrument ID
@@ -75,6 +76,24 @@ MaxCharge=5
 # If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
 NumMatchesPerSpec=1
 
+# Mass of charge carrier
+#  Default: mass of proton
+#ChargeCarrierMass=1.00727649
+
+# Maximum missed cleavages
+#  Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
+#MaxMissedCleavages=-1
+
+# Minimum number of ions a spectrum must have to be examined
+#MinNumPeaksPerSpectrum=10
+
+# Number of isoforms to consider per peptide
+#  Default: 128
+#NumIsoforms=128
+
+# Include additional features in the output (enable this to post-process results with Percolator)
+#AddFeatures=1
+
 # Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries

diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
@@ -1,9 +1,9 @@
-# Parent mass tolerance 
+# Precursor mass tolerance
 #  Examples: 2.5Da or 30ppm
 #  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
 PrecursorMassTolerance=20ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Dynamic (Variable) Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -19,7 +19,7 @@ DynamicMod=none
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID
@@ -77,6 +77,24 @@ MaxCharge=5
 # If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
 NumMatchesPerSpec=1
 
+# Mass of charge carrier
+#  Default: mass of proton
+#ChargeCarrierMass=1.00727649
+
+# Maximum missed cleavages
+#  Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
+#MaxMissedCleavages=-1
+
+# Minimum number of ions a spectrum must have to be examined
+#MinNumPeaksPerSpectrum=10
+
+# Number of isoforms to consider per peptide
+#  Default: 128
+#NumIsoforms=128
+
+# Include additional features in the output (enable this to post-process results with Percolator)
+#AddFeatures=1
+
 # Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries

diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
@@ -19,7 +19,7 @@ DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized meth
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID

diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_DynSTYPhos_Stat_CysAlk_TMT_6Plex_Protocol1_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_DynSTYPhos_Stat_CysAlk_TMT_6Plex_Protocol1_20ppmParTol.txt
@@ -1,9 +1,9 @@
-# Parent mass tolerance 
+# Precursor mass tolerance
 #  Examples: 2.5Da or 30ppm
 #  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
 PrecursorMassTolerance=20ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Dynamic (Variable) Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -19,7 +19,7 @@ DynamicMod=HO3P, STY, opt, any,            Phospho               # Phosphorylati
 #  1 means CID
 #  2 means ETD
 #  3 means HCD
-#  4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
 FragmentationMethodID=0
 
 # Instrument ID
@@ -85,6 +85,24 @@ NumMatchesPerSpec=1
 # MS-GF+ will auto-select the protocol based on the dynamic and static mods in place, so this generally does not need to be defined
 Protocol=1
 
+# Mass of charge carrier
+#  Default: mass of proton
+#ChargeCarrierMass=1.00727649
+
+# Maximum missed cleavages
+#  Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
+#MaxMissedCleavages=-1
+
+# Minimum number of ions a spectrum must have to be examined
+#MinNumPeaksPerSpectrum=10
+
+# Number of isoforms to consider per peptide
+#  Default: 128
+#NumIsoforms=128
+
+# Include additional features in the output (enable this to post-process results with Percolator)
+#AddFeatures=1
+
 # Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries