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 index 65933dd7..ce6a7977 100644 --- 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 @@ -1,20 +1,20 @@ -#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 (expMasstheoMass) 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 @@ -22,20 +22,20 @@ DynamicMod=O1, MP, opt, any, Oxidation # Oxidized methionine and prol # 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 @@ -43,44 +43,51 @@ EnzymeID=1 # 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 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 index 04817253..cfae31bf 100644 --- a/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt @@ -1,20 +1,20 @@ -#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 (expMasstheoMass) 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 @@ -22,20 +22,20 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth # 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 @@ -43,46 +43,51 @@ EnzymeID=1 # 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 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 index 7ccac25f..df0dd9db 100644 --- a/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt @@ -1,20 +1,20 @@ -#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 (expMasstheoMass) 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 @@ -22,20 +22,20 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine # 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 @@ -43,44 +43,51 @@ EnzymeID=1 # 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 diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt index 85ef611f..4f9be766 100644 --- a/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_TMT_6Plex_20ppmParTol.txt @@ -1,19 +1,19 @@ -#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 (expMasstheoMass) 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 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 @@ -21,20 +21,20 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth # 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 @@ -42,44 +42,51 @@ EnzymeID=1 # 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 -# 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 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 index c6eea8b1..acf9810a 100644 --- a/docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_CustomAA_O_Hydroxyproline_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_PartTryp_Dyn_MetOx_CustomAA_O_Hydroxyproline_20ppmParTol.txt @@ -1,21 +1,21 @@ -#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 (expMasstheoMass) 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=None DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine -#Custom amino acids +# Custom amino acids CustomAA=C5H7N1O2S0, O, custom, P, Hydroxylation # Hydroxyproline -#Fragmentation Method +# Fragmentation Method # 0 means as written in the spectrum or CID if no info (Default) # 1 means CID # 2 means ETD @@ -23,20 +23,20 @@ CustomAA=C5H7N1O2S0, O, custom, P, Hydroxylation # Hydroxyproline # 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 @@ -44,44 +44,51 @@ EnzymeID=1 # 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 -# 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 @@ -91,12 +98,13 @@ NumMatchesPerSpec=1 # H-3N-1, Q, opt, N-term, Gln->pyro-Glu # Pyro-glu from Q # C2H2O, *, opt, Prot-N-term, Acetyl # Acetylation Protein N-term -#Custom amino acids examples +# Custom amino acids examples # Only supports empirical formulas of elements C H N O S. # If other elements are needed, or a specific mass is needed, they can be added as fixed modifications on the custom AA # Maximum atom counts: 255 C, 255 H, 63 N, 63 O, 15 S # Format spec is: -# EmpiricalFormula, ResidueSymbol, custom, OriginalAA, Name (all the five fields are required, though OriginalAA is not actually used for anything) +# EmpiricalFormula, ResidueSymbol, custom, OriginalAA, Name (all five fields are required, though OriginalAA is not actually used for anything) +# # Examples: # C5H7N1O2S0,J,custom,P,Hydroxylation # Hydroxyproline # C3H6N2O0S1,X,custom,C,Amidation # C-terminal amidation of Cys 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 index 305fb7dc..4a829cba 100644 --- 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 @@ -1,20 +1,20 @@ -#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 (expMasstheoMass) 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=C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation) DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine or tryptophan (+15.9949) DynamicMod=C2H2O, *, opt, Prot-N-term, Acetyl # Acetylation Protein N-term (+42.0106) DynamicMod=H-1N-1O1, NQR, opt, any, Deamidated # Deamidation of Glutamine (+0.984016) -#Fragmentation Method +# Fragmentation Method # 0 means as written in the spectrum or CID if no info (Default) # 1 means CID # 2 means ETD @@ -22,20 +22,20 @@ DynamicMod=H-1N-1O1, NQR, opt, any, Deamidated # Deamidation of Gluta # 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 @@ -43,44 +43,51 @@ EnzymeID=1 # 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 -# 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 diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt index d043ef23..75b53fc2 100644 --- a/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_20ppmParTol.txt @@ -1,38 +1,38 @@ -#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 (expMasstheoMass) 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=None 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 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 @@ -40,46 +40,51 @@ EnzymeID=1 # 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 diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt index 5cbdb872..ef5032e6 100644 --- a/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_PartTryp_MetOx_StatCysAlk_20ppmParTol.txt @@ -1,18 +1,18 @@ -#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 (expMasstheoMass) 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=C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation) 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 @@ -20,20 +20,20 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionin # 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 @@ -41,46 +41,51 @@ EnzymeID=1 # 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 +# 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 diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt index eaf5823b..245c2190 100644 --- a/docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_PartTryp_StatCysAlk_20ppmParTol.txt @@ -1,18 +1,18 @@ -#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 (expMasstheoMass) 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=C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation) DynamicMod=None -#Fragmentation Method +# Fragmentation Method # 0 means as written in the spectrum or CID if no info (Default) # 1 means CID # 2 means ETD @@ -20,20 +20,20 @@ DynamicMod=None # 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 @@ -41,44 +41,51 @@ EnzymeID=1 # 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 diff --git a/docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt index aec9ecb3..de0eb568 100644 --- a/docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_PartTryp_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt @@ -1,20 +1,20 @@ -#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 (expMasstheoMass) 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=none -#Fragmentation Method +# Fragmentation Method # 0 means as written in the spectrum or CID if no info (Default) # 1 means CID # 2 means ETD @@ -22,20 +22,20 @@ DynamicMod=none # 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 @@ -43,44 +43,51 @@ EnzymeID=1 # 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 -# 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 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 index 887ce019..16f9ee18 100644 --- a/docs/ParameterFiles/MSGFPlus_Tryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_Tryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt @@ -1,20 +1,20 @@ -#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 (expMasstheoMass) 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 @@ -22,20 +22,20 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized meth # 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 @@ -43,46 +43,51 @@ EnzymeID=1 # 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=2 -#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 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 index a491163e..9fb0fbc8 100644 --- 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 @@ -1,20 +1,20 @@ -#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 (expMasstheoMass) 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=HO3P, STY, opt, any, Phospho # Phosphorylation STY -#Fragmentation Method +# Fragmentation Method # 0 means as written in the spectrum or CID if no info (Default) # 1 means CID # 2 means ETD @@ -22,20 +22,20 @@ DynamicMod=HO3P, STY, opt, any, Phospho # Phosphorylati # 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 @@ -43,52 +43,59 @@ EnzymeID=1 # 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=2 -#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 -#Scoring protocol to use; options are: +# Scoring protocol to use; options are: # 0=NoProtocol (Default) # 1=Phosphorylation # 2=iTRAQ # 3=iTRAQPhospho -#MSGF+ will auto-select the protocol based on the dynamic and static mods in place, so this generally does not need to be defined +# 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 -#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 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 index 2c6ce51b..16e163ae 100644 --- a/docs/ParameterFiles/MSGFPlus_Tryp_Dyn_MetOx_STYPhos_Stat_CysAlk_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_Tryp_Dyn_MetOx_STYPhos_Stat_CysAlk_20ppmParTol.txt @@ -1,19 +1,19 @@ -#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 (expMasstheoMass) 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=C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation) DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine DynamicMod=HO3P, STY, opt, any, Phospho # Phosphorylation STY -#Fragmentation Method +# Fragmentation Method # 0 means as written in the spectrum or CID if no info (Default) # 1 means CID # 2 means ETD @@ -21,20 +21,20 @@ DynamicMod=HO3P, STY, opt, any, Phospho # Phosphorylation # 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 @@ -42,44 +42,51 @@ EnzymeID=1 # 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=2 -#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 diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_15ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_15ppmParTol.txt index d63fdb1a..d8ab0bf7 100644 --- a/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_15ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_15ppmParTol.txt @@ -1,18 +1,18 @@ -#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 (expMasstheoMass) 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 -#Modifications (see below for examples) +# Modifications (see below for examples) StaticMod=None 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 @@ -20,20 +20,20 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine # 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 @@ -41,44 +41,51 @@ EnzymeID=1 # 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=2 -#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 diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_StatCysAlk_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_StatCysAlk_20ppmParTol.txt index 538fb6bc..048889ec 100644 --- a/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_StatCysAlk_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_Tryp_MetOx_StatCysAlk_20ppmParTol.txt @@ -1,18 +1,18 @@ -#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 (expMasstheoMass) 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=C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation) 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 @@ -20,20 +20,20 @@ DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionin # 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 @@ -41,44 +41,51 @@ EnzymeID=1 # 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=2 -#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 diff --git a/docs/ParameterFiles/MSGFPlus_Tryp_NoMods_20ppmParTol.txt b/docs/ParameterFiles/MSGFPlus_Tryp_NoMods_20ppmParTol.txt index cf6ef28d..662a6556 100644 --- a/docs/ParameterFiles/MSGFPlus_Tryp_NoMods_20ppmParTol.txt +++ b/docs/ParameterFiles/MSGFPlus_Tryp_NoMods_20ppmParTol.txt @@ -1,18 +1,18 @@ -#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 (expMasstheoMass) 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=None DynamicMod=None -#Fragmentation Method +# Fragmentation Method # 0 means as written in the spectrum or CID if no info (Default) # 1 means CID # 2 means ETD @@ -20,20 +20,20 @@ DynamicMod=None # 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 @@ -41,46 +41,51 @@ EnzymeID=1 # 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=2 -#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 diff --git a/docs/examples/MSGFPlus_Params.txt b/docs/examples/MSGFPlus_Params.txt index 13d86fd7..b645b8d5 100644 --- a/docs/examples/MSGFPlus_Params.txt +++ b/docs/examples/MSGFPlus_Params.txt @@ -1,28 +1,28 @@ -#SpectrumFile +# SpectrumFile # *.mzML, *.mzXML, *.mgf, *.ms2, *.pkl or *_dta.txt # Spectra should be centroided (see below for MSConvert example). Profile spectra will be ignored. # Use of -s at the command line will override this filename #SpectrumFile=InstrumentFile.mzML -#FASTA file +# FASTA file # "*.fasta or *.fa or *.faa # Use of -d at the command line will override this filename #DatabaseFile=Proteins.fasta -#Prefix for decoy proteins in the FASTA file +# Prefix for decoy proteins in the FASTA file #DecoyPrefix=XXX -#Precursor 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 (expMasstheoMass) PrecursorMassTolerance=20ppm -#Max Number of Dynamic (Variable) Modifications per peptide +# Max Number of Dynamic (Variable) Modifications per peptide # Default: 3 # If this value is large, the search will be slow NumMods=3 -#Modifications (see below for examples) +# Modifications (see below for examples) StaticMod=C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation) StaticMod=229.1629, *, fix, N-term, TMT6plex StaticMod=229.1629, K, fix, any, TMT6plex @@ -30,31 +30,31 @@ StaticMod=229.1629, K, fix, any, TMT6plex DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine DynamicMod=-187.152366, K, opt, any, AcNoTMT # Residue tagged by MSGF+ with static TMT6, but is actually acetylated and does not have TMT -#Custom AA specification +# Custom AA specification #CustomAA=C3H5NO, U, custom, U, Selenocysteine # Custom amino acids can only have C, H, N, O, and S #CustomAA=C6H11NO, X, custom, X, Leu_Ile # Leucine or Isoleucine -#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 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 @@ -62,62 +62,67 @@ EnzymeID=1 # 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=2 -#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 concurrent threads to be executed +# Number of concurrent threads to be executed # Default: Number of available cores # To use three threads use NumThreads=3 NumThreads=All -#Minimum peptide length to consider +# Minimum peptide length to consider # Default: 6 MinPepLength=6 -#Maximum peptide length to consider +# Maximum peptide length to consider # Default: 40 MaxPepLength=50 -#Minimum precursor charge to consider (if not specified in the spectrum file) +# Minimum precursor charge to consider (if not specified in the spectrum file) # Default: 2 MinCharge=2 -#Maximum precursor charge to consider (if not specified in the spectrum file) +# Maximum precursor charge to consider (if not specified in the spectrum file) # Default: 3 MaxCharge=5 -#Number of matches per spectrum to be reported +# 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 -#Mass of charge carrier +# Mass of charge carrier # Default: mass of proton #ChargeCarrierMass=1.00727649 -#Maximum missed cleavages +# 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 peaks per spectrum, Default: +# Minimum number of peaks per spectrum, Default: # Default: 10 #MinNumPeaksPerSpectrum=10 -#Number of isoforms to consider per peptide +# Number of isoforms to consider per peptide # Default: 128 #NumIsoforms=128 -#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: