Update comments in example parameter files

Author: alchemistmatt

docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_ProOx_Stat_CysAlk_TMT_6Plex_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
 
@@ -15,18 +15,18 @@ StaticMod=C2H3N1O1,    C,  fix, any,      Carbamidomethyl       # Fixed Carbamid
 DynamicMod=O1, MP, opt, any, Oxidation            # Oxidized methionine and proline
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID

docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt

@@ -15,18 +15,18 @@ StaticMod=C2H3N1O1,    C,  fix, any,       Carbamidomethyl       # Fixed Carbami
 DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized methionine
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID

docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_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
 
@@ -15,18 +15,18 @@ StaticMod=C2H3N1O1,    C,  fix, any,      Carbamidomethyl       # Fixed Carbamid
 DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID

docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt

@@ -14,18 +14,18 @@ StaticMod=229.1629,    K,  fix, any,       TMT6plex
 DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized methionine
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID

docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_CustomAA_O_Hydroxyproline_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
 
@@ -16,18 +16,18 @@ DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 CustomAA=C5H7N1O2S0,   O,  custom, P, Hydroxylation     # Hydroxyproline
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID
@@ -107,5 +107,5 @@ NumMatchesPerSpec=1
 #
 # Examples:
 #   C5H7N1O2S0,J,custom,P,Hydroxylation     # Hydroxyproline
-#   C3H6N2O0S1,X,custom,C,Amidation         # C-terminal amidation of Cys  
+#   C3H6N2O0S1,X,custom,C,Amidation         # C-terminal amidation of Cys
 #   C5H5N1O1S0,Z,custom,E,Glu->pyro-Glu     # N-terminal pyroGlu residue, from either Glu OR Gln

docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_NTermAcet_NQR_Deamide_Stat_CysAlk_20ppmParTol.txt

@@ -15,18 +15,18 @@ 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 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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID

docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt

@@ -13,18 +13,18 @@ StaticMod=None
 DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID

docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt

@@ -13,18 +13,18 @@ StaticMod=C2H3N1O1,  C, fix, any, Carbamidomethyl           # Fixed Carbamidomet
 DynamicMod=O1,       M, opt, any, Oxidation                 # Oxidized methionine
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID

docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt

@@ -13,18 +13,18 @@ StaticMod=C2H3N1O1,  C, fix, any, Carbamidomethyl          # Fixed Carbamidometh
 DynamicMod=None
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID

docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt

@@ -15,18 +15,18 @@ StaticMod=C2H3N1O1,    C,  fix, any,       Carbamidomethyl       # Fixed Carbami
 DynamicMod=none
 
 # Fragmentation Method
-#  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
+#  0 means as written in the spectrum or CID if no info (Default)
+#  1 means CID
+#  2 means ETD
+#  3 means HCD
 #  4 means UVPD
 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, Lumos, and QEHFX instruments
+#  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
 #  2 means TOF
-#  3 means Q-Exactive
+#  3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
 InstrumentID=1
 
 # Enzyme ID