Update example parameter files

docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_ProOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt

@@ -1,86 +1,93 @@
-#Parent mass tolerance 
+# Parent 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 Modifications per peptide 
 # If this value is large, the search will be slow
 NumMods=3
 
-#Modifications (see below for examples)
+# Modifications (see below for examples)
 StaticMod=229.1629,  *,  fix, N-term,   TMT6plex
 StaticMod=229.1629,  K,  fix, any,      TMT6plex
 StaticMod=C2H3N1O1,    C,  fix, any,      Carbamidomethyl       # Fixed Carbamidomethyl C (alkylation, +57.0215)
 
 DynamicMod=O1, MP, opt, any, Oxidation            # Oxidized methionine and proline
 
-#Fragmentation Method
+# Fragmentation Method
 #  0 means as written in the spectrum or CID if no info (Default)
 #  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) 
 FragmentationMethodID=0
 
-#Instrument ID
+# 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
 #  2 means TOF
 #  3 means Q-Exactive
 InstrumentID=1
 
-#Enzyme ID
-#  0 means No enzyme used
-#  1 means Trypsin (Default); use this along with NTT=0 for a no-enzyme search of a tryptically digested sample
-#  2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Enzyme (for peptidomics)
+# Enzyme ID
+#  0 means unspecific cleavage (cleave after any residue)
+#  1 means Trypsin (Default); optionally use this along with NTT=0 for a no-enzyme-specificity search of a tryptically digested sample
+#  2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Cleavage (for peptidomics)
 EnzymeID=1
 
-#Isotope error range
+# Isotope error range
 #  Takes into account of the error introduced by choosing non-monoisotopic peak for fragmentation.
 #  Useful for accurate precursor ion masses
 #  Ignored if the parent mass tolerance is > 0.5Da or 500ppm
 #  The combination of -t and -ti determins the precursor mass tolerance.
 #  e.g. "-t 20ppm -ti -1,2" tests abs(exp-calc-n*1.00335Da)<20ppm for n=-1, 0, 1, 2.
 IsotopeErrorRange=-1,1
 
-#Number of tolerable termini
+# Number of tolerable termini
 #  The number of peptide termini that must have been cleaved by the enzyme (default 1)
 #  For trypsin, 2 means fully tryptic only, 1 means partially tryptic, and 0 means no-enzyme search
 NTT=1
 
-#Target/Decoy search mode
+# Control N-terminal methionine cleavage
+#  0 means to consider protein N-term Met cleavage (Default)
+#  1 means to ignore protein N-term Met cleavage
+IgnoreMetCleavage=0
+
+# Target/Decoy search mode
 #  0 means don't search decoy database (default)
 #  1 means search decoy database to compute FDR (source FASTA file must be forward-only proteins)
 TDA=1
 
-#Number of Threads (by default, uses all available cores)
+# Number of Threads (by default, uses all available cores)
 NumThreads=All
 
-#Minimum peptide length to consider
+# Minimum peptide length to consider
 MinPepLength=6
 
-#Maximum peptide length to consider
+# Maximum peptide length to consider
 MaxPepLength=50
 
-#Minimum precursor charge to consider (if not specified in the spectrum)
+# Minimum precursor charge to consider (if not specified in the spectrum)
 MinCharge=2
 
-#Maximum precursor charge to consider (if not specified in the spectrum)
+# Maximum precursor charge to consider (if not specified in the spectrum)
 MaxCharge=5
 
-#Number of matches per spectrum to be reported
-#If this value is greater than 1 then the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
+# Number of matches per spectrum to be reported
+# 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
 
-#Amino Acid Modification Examples
-# Specific static modifications using one or more StaticMod= entries
-# Specific dynamic modifications using one or more DynamicMod= entries
+# Amino Acid Modification Examples
+# Specify static modifications using one or more StaticMod= entries
+# Specify dynamic modifications using one or more DynamicMod= entries
 # Modification format is:
-# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
+# Mass or CompositionString, Residues, ModType, Position, Name (all five fields are required).
+# CompositionString can only contain a limited set of elements, primarily C H N O S or P
+#
 # Examples:
 #   C2H3N1O1,  C,  fix, any,         Carbamidomethyl    # Fixed Carbamidomethyl C (alkylation)
 #   O1,        M,  opt, any,         Oxidation          # Oxidation M
-#   15.994915, M,  opt, any,         Oxidation          # Oxidation M (mass is used instead of CompositionStr)
+#   15.994915, M,  opt, any,         Oxidation          # Oxidation M (mass is used instead of CompositionString)
 #   H-1N-1O1,  NQ, opt, any,         Deamidated         # Negative numbers are allowed.
 #   CH2,       K,  opt, any,         Methyl             # Methylation K
 #   C2H2O1,    K,  opt, any,         Acetyl             # Acetylation K

docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt

@@ -1,88 +1,93 @@
-#Parent mass tolerance 
+# Parent 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 Modifications per peptide 
 # If this value is large, the search will be slow
 NumMods=3
 
-#Modifications (see below for examples)
+# Modifications (see below for examples)
 StaticMod=229.1629,    *,  fix, N-term,    TMT6plex
 StaticMod=229.1629,    K,  fix, any,       TMT6plex
 StaticMod=C2H3N1O1,    C,  fix, any,       Carbamidomethyl       # Fixed Carbamidomethyl C (alkylation, +57.0215)
 
 DynamicMod=O1, M, opt, any,                Oxidation             # Oxidized methionine
 
-#Fragmentation Method
+# Fragmentation Method
 #  0 means as written in the spectrum or CID if no info (Default)
 #  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) 
 FragmentationMethodID=0
 
-#Instrument ID
+# 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
 #  2 means TOF
 #  3 means Q-Exactive
 InstrumentID=1
 
-#Enzyme ID
-#  0 means No enzyme used
-#  1 means Trypsin (Default); use this along with NTT=0 for a no-enzyme search of a tryptically digested sample
-#  2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Enzyme (for peptidomics)
+# Enzyme ID
+#  0 means unspecific cleavage (cleave after any residue)
+#  1 means Trypsin (Default); optionally use this along with NTT=0 for a no-enzyme-specificity search of a tryptically digested sample
+#  2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Cleavage (for peptidomics)
 EnzymeID=1
 
-#Isotope error range
+# Isotope error range
 #  Takes into account of the error introduced by choosing non-monoisotopic peak for fragmentation.
 #  Useful for accurate precursor ion masses
 #  Ignored if the parent mass tolerance is > 0.5Da or 500ppm
 #  The combination of -t and -ti determins the precursor mass tolerance.
 #  e.g. "-t 20ppm -ti -1,2" tests abs(exp-calc-n*1.00335Da)<20ppm for n=-1, 0, 1, 2.
 IsotopeErrorRange=-1,2
 
-#Number of tolerable termini
+# Number of tolerable termini
 #  The number of peptide termini that must have been cleaved by the enzyme (default 1)
 #  For trypsin, 2 means fully tryptic only, 1 means partially tryptic, and 0 means no-enzyme search
 NTT=1
 
-#Target/Decoy search mode
+# Control N-terminal methionine cleavage
+#  0 means to consider protein N-term Met cleavage (Default)
+#  1 means to ignore protein N-term Met cleavage
+IgnoreMetCleavage=0
+
+# Target/Decoy search mode
 #  0 means don't search decoy database (default)
 #  1 means search decoy database to compute FDR (source FASTA file must be forward-only proteins)
 TDA=1
 
-#Number of Threads (by default, uses all available cores)
+# Number of Threads (by default, uses all available cores)
 NumThreads=All
 
-#Minimum peptide length to consider
+# Minimum peptide length to consider
 MinPepLength=6
 
-#Maximum peptide length to consider
+# Maximum peptide length to consider
 MaxPepLength=50
 
-#Minimum precursor charge to consider (if not specified in the spectrum)
+# Minimum precursor charge to consider (if not specified in the spectrum)
 MinCharge=2
 
-#Maximum precursor charge to consider (if not specified in the spectrum)
+# Maximum precursor charge to consider (if not specified in the spectrum)
 MaxCharge=5
 
-#Number of matches per spectrum to be reported
-#If this value is greater than 1 then the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
+# Number of matches per spectrum to be reported
+# 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
 
-#Amino Acid Modification Examples
+# Amino Acid Modification Examples
 # Specify static modifications using one or more StaticMod= entries
 # Specify dynamic modifications using one or more DynamicMod= entries
 # Modification format is:
-# Mass or CompositionString, Residues, ModType, Position, Name (all the five fields are required).
+# Mass or CompositionString, Residues, ModType, Position, Name (all five fields are required).
 # CompositionString can only contain a limited set of elements, primarily C H N O S or P
 #
 # Examples:
 #   C2H3N1O1,  C,  fix, any,         Carbamidomethyl    # Fixed Carbamidomethyl C (alkylation)
 #   O1,        M,  opt, any,         Oxidation          # Oxidation M
-#   15.994915, M,  opt, any,         Oxidation          # Oxidation M (mass is used instead of CompositionStr)
+#   15.994915, M,  opt, any,         Oxidation          # Oxidation M (mass is used instead of CompositionString)
 #   H-1N-1O1,  NQ, opt, any,         Deamidated         # Negative numbers are allowed.
 #   CH2,       K,  opt, any,         Methyl             # Methylation K
 #   C2H2O1,    K,  opt, any,         Acetyl             # Acetylation K

docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt

@@ -1,86 +1,93 @@
-#Parent mass tolerance 
+# Parent 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 Modifications per peptide 
 # If this value is large, the search will be slow
 NumMods=3
 
-#Modifications (see below for examples)
+# Modifications (see below for examples)
 StaticMod=304.205353,  *,  fix, N-term,   iTRAQ8plex
 StaticMod=304.205353,  K,  fix, any,      iTRAQ8plex
 StaticMod=C2H3N1O1,    C,  fix, any,      Carbamidomethyl       # Fixed Carbamidomethyl C (alkylation, +57.0215)
 
 DynamicMod=O1, M, opt, any, Oxidation            # Oxidized methionine
 
-#Fragmentation Method
+# Fragmentation Method
 #  0 means as written in the spectrum or CID if no info (Default)
 #  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) 
 FragmentationMethodID=0
 
-#Instrument ID
+# 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
 #  2 means TOF
 #  3 means Q-Exactive
 InstrumentID=1
 
-#Enzyme ID
-#  0 means No enzyme used
-#  1 means Trypsin (Default); use this along with NTT=0 for a no-enzyme search of a tryptically digested sample
-#  2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Enzyme (for peptidomics)
+# Enzyme ID
+#  0 means unspecific cleavage (cleave after any residue)
+#  1 means Trypsin (Default); optionally use this along with NTT=0 for a no-enzyme-specificity search of a tryptically digested sample
+#  2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Cleavage (for peptidomics)
 EnzymeID=1
 
-#Isotope error range
+# Isotope error range
 #  Takes into account of the error introduced by choosing non-monoisotopic peak for fragmentation.
 #  Useful for accurate precursor ion masses
 #  Ignored if the parent mass tolerance is > 0.5Da or 500ppm
 #  The combination of -t and -ti determins the precursor mass tolerance.
 #  e.g. "-t 20ppm -ti -1,2" tests abs(exp-calc-n*1.00335Da)<20ppm for n=-1, 0, 1, 2.
 IsotopeErrorRange=-1,1
 
-#Number of tolerable termini
+# Number of tolerable termini
 #  The number of peptide termini that must have been cleaved by the enzyme (default 1)
 #  For trypsin, 2 means fully tryptic only, 1 means partially tryptic, and 0 means no-enzyme search
 NTT=1
 
-#Target/Decoy search mode
+# Control N-terminal methionine cleavage
+#  0 means to consider protein N-term Met cleavage (Default)
+#  1 means to ignore protein N-term Met cleavage
+IgnoreMetCleavage=0
+
+# Target/Decoy search mode
 #  0 means don't search decoy database (default)
 #  1 means search decoy database to compute FDR (source FASTA file must be forward-only proteins)
 TDA=1
 
-#Number of Threads (by default, uses all available cores)
+# Number of Threads (by default, uses all available cores)
 NumThreads=All
 
-#Minimum peptide length to consider
+# Minimum peptide length to consider
 MinPepLength=6
 
-#Maximum peptide length to consider
+# Maximum peptide length to consider
 MaxPepLength=50
 
-#Minimum precursor charge to consider (if not specified in the spectrum)
+# Minimum precursor charge to consider (if not specified in the spectrum)
 MinCharge=2
 
-#Maximum precursor charge to consider (if not specified in the spectrum)
+# Maximum precursor charge to consider (if not specified in the spectrum)
 MaxCharge=5
 
-#Number of matches per spectrum to be reported
-#If this value is greater than 1 then the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
+# Number of matches per spectrum to be reported
+# 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
 
-#Amino Acid Modification Examples
-# Specific static modifications using one or more StaticMod= entries
-# Specific dynamic modifications using one or more DynamicMod= entries
+# Amino Acid Modification Examples
+# Specify static modifications using one or more StaticMod= entries
+# Specify dynamic modifications using one or more DynamicMod= entries
 # Modification format is:
-# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
+# Mass or CompositionString, Residues, ModType, Position, Name (all five fields are required).
+# CompositionString can only contain a limited set of elements, primarily C H N O S or P
+#
 # Examples:
 #   C2H3N1O1,  C,  fix, any,         Carbamidomethyl    # Fixed Carbamidomethyl C (alkylation)
 #   O1,        M,  opt, any,         Oxidation          # Oxidation M
-#   15.994915, M,  opt, any,         Oxidation          # Oxidation M (mass is used instead of CompositionStr)
+#   15.994915, M,  opt, any,         Oxidation          # Oxidation M (mass is used instead of CompositionString)
 #   H-1N-1O1,  NQ, opt, any,         Deamidated         # Negative numbers are allowed.
 #   CH2,       K,  opt, any,         Methyl             # Methylation K
 #   C2H2O1,    K,  opt, any,         Acetyl             # Acetylation K