# 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 or *.fa or *.faa
#  Use of -d at the command line will override this filename
DatabaseFile=E:\JB\salted_PPutidaKT2440_LysC_unique_shortHeader_inclDecoys_Unique.fasta

# Prefix for decoy proteins in the FASTA file
DecoyPrefix=DECOY_

# Precursor mass tolerance
#  Examples: 2.5Da or 30ppm
#  Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
PrecursorMassTolerance=10ppm

# Max Number of Dynamic (Variable) Modifications per peptide
#  Default: 3
#  If this value is large, the search will be slow
NumMods=5

# Modifications (see below for examples)
StaticMod=57.021464,     C,  fix, any,       Carbamidomethyl       # Fixed Carbamidomethyl C (alkylation)
DynamicMod=15.994915,     M,   opt, any,         Oxidation M        # Oxidation M
DynamicMod=-17.026549,    Q,   opt, N-term,      Gln->pyro-Glu      # Pyro-glu from Q
DynamicMod=-18.010565,   E,   opt, N-term,      Glu->pyro-Glu      # Pyro-glu from E


# 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
#  0 means as written in the spectrum or CID if no info (Default)
#  1 means CID
#  2 means ETD
#  3 means HCD
FragmentationMethodID=3

# 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=3

# 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=3

# Isotope error range
#  Takes into account of the error introduced by choosing non-monoisotopic peak for fragmentation.
#  Useful for accurate precursor ion masses
#  Ignored if the parent mass tolerance is > 0.5Da or 500ppm
#  The combination of -t and -ti determins the precursor mass tolerance.
#  e.g. "-t 20ppm -ti -1,2" tests abs(exp-calc-n*1.00335Da)<20ppm for n=-1, 0, 1, 2.
IsotopeErrorRange=0,3

# 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

# 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=0

# 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
#  Default: 6
MinPepLength=5

# Maximum peptide length to consider
#  Default: 40
MaxPepLength=50

# 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)
#  Default: 3
MaxCharge=6

# 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
#  Default: mass of proton
#ChargeCarrierMass=1.00727649

# 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:
#  Default: 10
#MinNumPeaksPerSpectrum=10

# Number of isoforms to consider per peptide
#  Default: 128
#NumIsoforms=128

# 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 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 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
#   HO3P,      STY,opt, any,         Phospho            # Phosphorylation STY
#   C2H3NO,    *,  opt, N-term,      Carbamidomethyl    # Variable Carbamidomethyl N-term
#   H-2O-1,    E,  opt, N-term,      Glu->pyro-Glu      # Pyro-glu from E
#   H-3N-1,    Q,  opt, N-term,      Gln->pyro-Glu      # Pyro-glu from Q
#   C2H2O,     *,  opt, Prot-N-term, Acetyl             # Acetylation Protein N-term