Update comments in parameter files

alchemistmatt · alchemistmatt · commit 8af811f0723c · 2022-01-07T20:45:35.000-08:00
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
@@ -1,4 +1,4 @@
-# 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
@@ -15,11 +15,11 @@ StaticMod=C2H3N1O1,    C,  fix, any,      Carbamidomethyl       # Fixed Carbamid
 DynamicMod=O1, MP, opt, any, Oxidation            # Oxidized methionine and proline
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 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
@@ -15,11 +15,11 @@ StaticMod=C2H3N1O1,    C,  fix, any,       Carbamidomethyl       # Fixed Carbami
 DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized methionine
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
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
@@ -1,4 +1,4 @@
-# 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
@@ -15,11 +15,11 @@ StaticMod=C2H3N1O1,    C,  fix, any,      Carbamidomethyl       # Fixed Carbamid
 DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 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
@@ -14,11 +14,11 @@ StaticMod=229.1629,    K,  fix, any,       TMT6plex
 DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized methionine
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
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
@@ -1,4 +1,4 @@
-# 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
@@ -16,11 +16,11 @@ DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 CustomAA=C5H7N1O2S0,   O,  custom, P, Hydroxylation     # Hydroxyproline
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_NTermAcet_NQR_Deamide_Stat_CysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_NTermAcet_NQR_Deamide_Stat_CysAlk_20ppmParTol.txt
@@ -1,4 +1,4 @@
-# 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
@@ -15,11 +15,11 @@ DynamicMod=C2H2O,    *,   opt, Prot-N-term, Acetyl          # Acetylation Protei
 DynamicMod=H-1N-1O1, NQR, opt, any, Deamidated           	# Deamidation of Glutamine (+0.984016)
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets)
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt
@@ -13,10 +13,11 @@ StaticMod=None
 DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt
@@ -13,11 +13,11 @@ StaticMod=C2H3N1O1,  C, fix, any, Carbamidomethyl           # Fixed Carbamidomet
 DynamicMod=O1,       M, opt, any, Oxidation                 # Oxidized methionine
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt
@@ -13,12 +13,11 @@ StaticMod=C2H3N1O1,  C, fix, any, Carbamidomethyl          # Fixed Carbamidometh
 DynamicMod=None
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  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)
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
@@ -15,11 +15,11 @@ StaticMod=C2H3N1O1,    C,  fix, any,       Carbamidomethyl       # Fixed Carbami
 DynamicMod=none
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
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
@@ -1,4 +1,4 @@
-# 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
@@ -15,11 +15,11 @@ StaticMod=C2H3N1O1,    C,  fix, any,       Carbamidomethyl       # Fixed Carbami
 DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized methionine
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 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
@@ -15,11 +15,11 @@ StaticMod=C2H3N1O1,    C,  fix, any,       Carbamidomethyl       # Fixed Carbami
 DynamicMod=HO3P, STY, opt, any,            Phospho               # Phosphorylation STY
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_Dyn_MetOx_STYPhos_Stat_CysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_Dyn_MetOx_STYPhos_Stat_CysAlk_20ppmParTol.txt
@@ -14,11 +14,11 @@ DynamicMod=O1,       M,   opt, any, Oxidation                 # Oxidized methion
 DynamicMod=HO3P,     STY, opt, any, Phospho                   # Phosphorylation STY
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_15ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_15ppmParTol.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=15ppm
 
-# Max Number of Modifications per peptide 
+# Max Number of Modifications per peptide
 # If this value is large, the search will be slow
 NumMods=3
 
@@ -13,11 +13,11 @@ StaticMod=None
 DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_StatCysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_StatCysAlk_20ppmParTol.txt
@@ -13,11 +13,11 @@ StaticMod=C2H3N1O1,  C, fix, any, Carbamidomethyl           # Fixed Carbamidomet
 DynamicMod=O1,       M, opt, any, Oxidation                 # Oxidized methionine
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_NoMods_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_NoMods_20ppmParTol.txt
@@ -13,11 +13,11 @@ StaticMod=None
 DynamicMod=None
 
 # Fragmentation Method
-#  0 means as written in the spectrum or CID if no info (Default)
-#  1 means CID
-#  2 means ETD
-#  3 means HCD
-#  Disabled in MS-GF+: 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) 
+#  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 with high res MS2 spectra
+#  2 means TOF
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
+#  4 means UVPD
 FragmentationMethodID=0
 
 # Instrument ID
