Skip to content

Commit f846ded

Browse files
alchemistmattalchemistmatt
committed
Update comments in MS-GF+ parameter files
1 parent 4fa1ed9 commit f846ded

16 files changed

+254
-37
lines changed

‎docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_ProOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ DynamicMod=O1, MP, opt, any, Oxidation # Oxidized methionine and prol
1919
# 1 means CID
2020
# 2 means ETD
2121
# 3 means HCD
22-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
22+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
2323
FragmentationMethodID=0
2424

2525
# Instrument ID

‎docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt‎

Lines changed: 21 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
1-
# Parent mass tolerance
1+
# Precursor mass tolerance
22
# Examples: 2.5Da or 30ppm
33
# 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)
44
PrecursorMassTolerance=20ppm
55

6-
# Max Number of Modifications per peptide
6+
# Max Number of Dynamic (Variable) Modifications per peptide
77
# If this value is large, the search will be slow
88
NumMods=3
99

@@ -19,7 +19,7 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth
1919
# 1 means CID
2020
# 2 means ETD
2121
# 3 means HCD
22-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
22+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
2323
FragmentationMethodID=0
2424

2525
# Instrument ID
@@ -77,6 +77,24 @@ MaxCharge=5
7777
# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
7878
NumMatchesPerSpec=1
7979

80+
# Mass of charge carrier
81+
# Default: mass of proton
82+
#ChargeCarrierMass=1.00727649
83+
84+
# Maximum missed cleavages
85+
# Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
86+
#MaxMissedCleavages=-1
87+
88+
# Minimum number of ions a spectrum must have to be examined
89+
#MinNumPeaksPerSpectrum=10
90+
91+
# Number of isoforms to consider per peptide
92+
# Default: 128
93+
#NumIsoforms=128
94+
95+
# Include additional features in the output (enable this to post-process results with Percolator)
96+
#AddFeatures=1
97+
8098
# Amino Acid Modification Examples
8199
# Specify static modifications using one or more StaticMod= entries
82100
# Specify dynamic modifications using one or more DynamicMod= entries

‎docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine
1919
# 1 means CID
2020
# 2 means ETD
2121
# 3 means HCD
22-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
22+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
2323
FragmentationMethodID=0
2424

2525
# Instrument ID

‎docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt‎

Lines changed: 21 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
1-
# Parent mass tolerance
1+
# Precursor mass tolerance
22
# Examples: 2.5Da or 30ppm
33
# 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)
44
PrecursorMassTolerance=20ppm
55

6-
# Max Number of Modifications per peptide
6+
# Max Number of Dynamic (Variable) Modifications per peptide
77
# If this value is large, the search will be slow
88
NumMods=3
99

@@ -18,7 +18,7 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth
1818
# 1 means CID
1919
# 2 means ETD
2020
# 3 means HCD
21-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
21+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
2222
FragmentationMethodID=0
2323

2424
# Instrument ID
@@ -76,6 +76,24 @@ MaxCharge=5
7676
# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
7777
NumMatchesPerSpec=1
7878

79+
# Mass of charge carrier
80+
# Default: mass of proton
81+
#ChargeCarrierMass=1.00727649
82+
83+
# Maximum missed cleavages
84+
# Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
85+
#MaxMissedCleavages=-1
86+
87+
# Minimum number of ions a spectrum must have to be examined
88+
#MinNumPeaksPerSpectrum=10
89+
90+
# Number of isoforms to consider per peptide
91+
# Default: 128
92+
#NumIsoforms=128
93+
94+
# Include additional features in the output (enable this to post-process results with Percolator)
95+
#AddFeatures=1
96+
7997
# Amino Acid Modification Examples
8098
# Specify static modifications using one or more StaticMod= entries
8199
# Specify dynamic modifications using one or more DynamicMod= entries

‎docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_CustomAA_O_Hydroxyproline_20ppmParTol.txt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ CustomAA=C5H7N1O2S0, O, custom, P, Hydroxylation # Hydroxyproline
2020
# 1 means CID
2121
# 2 means ETD
2222
# 3 means HCD
23-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
23+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
2424
FragmentationMethodID=0
2525

2626
# Instrument ID

‎docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_NTermAcet_NQR_Deamide_Stat_CysAlk_20ppmParTol.txt‎

Lines changed: 20 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
# 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)
44
PrecursorMassTolerance=20ppm
55

6-
# Max Number of Modifications per peptide
6+
# Max Number of Dynamic (Variable) Modifications per peptide
77
# If this value is large, the search will be slow
88
NumMods=3
99

@@ -19,7 +19,7 @@ DynamicMod=H-1N-1O1, NQR, opt, any, Deamidated # Deamidation of Gluta
1919
# 1 means CID
2020
# 2 means ETD
2121
# 3 means HCD
22-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
22+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
2323
FragmentationMethodID=0
2424

2525
# Instrument ID
@@ -77,6 +77,24 @@ MaxCharge=5
7777
# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
7878
NumMatchesPerSpec=1
7979

80+
# Mass of charge carrier
81+
# Default: mass of proton
82+
#ChargeCarrierMass=1.00727649
83+
84+
# Maximum missed cleavages
85+
# Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
86+
#MaxMissedCleavages=-1
87+
88+
# Minimum number of ions a spectrum must have to be examined
89+
#MinNumPeaksPerSpectrum=10
90+
91+
# Number of isoforms to consider per peptide
92+
# Default: 128
93+
#NumIsoforms=128
94+
95+
# Include additional features in the output (enable this to post-process results with Percolator)
96+
#AddFeatures=1
97+
8098
# Amino Acid Modification Examples
8199
# Specify static modifications using one or more StaticMod= entries
82100
# Specify dynamic modifications using one or more DynamicMod= entries

‎docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt‎

Lines changed: 20 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
1-
# Parent mass tolerance
1+
# Precursor mass tolerance
22
# Examples: 2.5Da or 30ppm
33
# 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)
44
PrecursorMassTolerance=20ppm
55

6-
# Max Number of Modifications per peptide
6+
# Max Number of Dynamic (Variable) Modifications per peptide
77
# If this value is large, the search will be slow
88
NumMods=3
99

@@ -74,6 +74,24 @@ MaxCharge=5
7474
# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
7575
NumMatchesPerSpec=1
7676

77+
# Mass of charge carrier
78+
# Default: mass of proton
79+
#ChargeCarrierMass=1.00727649
80+
81+
# Maximum missed cleavages
82+
# Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
83+
#MaxMissedCleavages=-1
84+
85+
# Minimum number of ions a spectrum must have to be examined
86+
#MinNumPeaksPerSpectrum=10
87+
88+
# Number of isoforms to consider per peptide
89+
# Default: 128
90+
#NumIsoforms=128
91+
92+
# Include additional features in the output (enable this to post-process results with Percolator)
93+
#AddFeatures=1
94+
7795
# Amino Acid Modification Examples
7896
# Specify static modifications using one or more StaticMod= entries
7997
# Specify dynamic modifications using one or more DynamicMod= entries

‎docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt‎

Lines changed: 21 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
1-
# Parent mass tolerance
1+
# Precursor mass tolerance
22
# Examples: 2.5Da or 30ppm
33
# 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)
44
PrecursorMassTolerance=20ppm
55

6-
# Max Number of Modifications per peptide
6+
# Max Number of Dynamic (Variable) Modifications per peptide
77
# If this value is large, the search will be slow
88
NumMods=3
99

@@ -17,7 +17,7 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionin
1717
# 1 means CID
1818
# 2 means ETD
1919
# 3 means HCD
20-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
20+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
2121
FragmentationMethodID=0
2222

2323
# Instrument ID
@@ -75,6 +75,24 @@ MaxCharge=5
7575
# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
7676
NumMatchesPerSpec=1
7777

78+
# Mass of charge carrier
79+
# Default: mass of proton
80+
#ChargeCarrierMass=1.00727649
81+
82+
# Maximum missed cleavages
83+
# Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
84+
#MaxMissedCleavages=-1
85+
86+
# Minimum number of ions a spectrum must have to be examined
87+
MinNumPeaksPerSpectrum=5
88+
89+
# Number of isoforms to consider per peptide
90+
# Default: 128
91+
#NumIsoforms=128
92+
93+
# Include additional features in the output (enable this to post-process results with Percolator)
94+
AddFeatures=1
95+
7896
# Amino Acid Modification Examples
7997
# Specify static modifications using one or more StaticMod= entries
8098
# Specify dynamic modifications using one or more DynamicMod= entries

‎docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt‎

Lines changed: 22 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
1-
# Parent mass tolerance
1+
# Precursor mass tolerance
22
# Examples: 2.5Da or 30ppm
33
# 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)
44
PrecursorMassTolerance=20ppm
55

6-
# Max Number of Modifications per peptide
6+
# Max Number of Dynamic (Variable) Modifications per peptide
77
# If this value is large, the search will be slow
88
NumMods=3
99

@@ -17,7 +17,8 @@ DynamicMod=None
1717
# 1 means CID
1818
# 2 means ETD
1919
# 3 means HCD
20-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
20+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
21+
# (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)
2122
FragmentationMethodID=0
2223

2324
# Instrument ID
@@ -75,6 +76,24 @@ MaxCharge=5
7576
# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
7677
NumMatchesPerSpec=1
7778

79+
# Mass of charge carrier
80+
# Default: mass of proton
81+
#ChargeCarrierMass=1.00727649
82+
83+
# Maximum missed cleavages
84+
# Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
85+
#MaxMissedCleavages=-1
86+
87+
# Minimum number of ions a spectrum must have to be examined
88+
#MinNumPeaksPerSpectrum=10
89+
90+
# Number of isoforms to consider per peptide
91+
# Default: 128
92+
#NumIsoforms=128
93+
94+
# Include additional features in the output (enable this to post-process results with Percolator)
95+
#AddFeatures=1
96+
7897
# Amino Acid Modification Examples
7998
# Specify static modifications using one or more StaticMod= entries
8099
# Specify dynamic modifications using one or more DynamicMod= entries

‎docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt‎

Lines changed: 21 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
1-
# Parent mass tolerance
1+
# Precursor mass tolerance
22
# Examples: 2.5Da or 30ppm
33
# 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)
44
PrecursorMassTolerance=20ppm
55

6-
# Max Number of Modifications per peptide
6+
# Max Number of Dynamic (Variable) Modifications per peptide
77
# If this value is large, the search will be slow
88
NumMods=3
99

@@ -19,7 +19,7 @@ DynamicMod=none
1919
# 1 means CID
2020
# 2 means ETD
2121
# 3 means HCD
22-
# 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
22+
# Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
2323
FragmentationMethodID=0
2424

2525
# Instrument ID
@@ -77,6 +77,24 @@ MaxCharge=5
7777
# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
7878
NumMatchesPerSpec=1
7979

80+
# Mass of charge carrier
81+
# Default: mass of proton
82+
#ChargeCarrierMass=1.00727649
83+
84+
# Maximum missed cleavages
85+
# Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
86+
#MaxMissedCleavages=-1
87+
88+
# Minimum number of ions a spectrum must have to be examined
89+
#MinNumPeaksPerSpectrum=10
90+
91+
# Number of isoforms to consider per peptide
92+
# Default: 128
93+
#NumIsoforms=128
94+
95+
# Include additional features in the output (enable this to post-process results with Percolator)
96+
#AddFeatures=1
97+
8098
# Amino Acid Modification Examples
8199
# Specify static modifications using one or more StaticMod= entries
82100
# Specify dynamic modifications using one or more DynamicMod= entries

0 commit comments

Comments
 (0)