From SPCTools
### COMMON OPTIONS ##############################
# Spectral library to be searched against - required if not specified on command-line with -sL option - replace with your own
libraryFile = /path/to/myLibrary.splib
# A database file to be included in .pepXML outputs for downstream TPP processing - replace with your own
databaseFile = /path/to/myDatabase.fasta
# The type of the database: "AA" = amino acid database; "DNA" = nucleotide database
databaseType = AA
# Selected List File Name - specify a file containing spectrum query names to be searched
filterSelectedListFileName =
# Whether to keep all accessed library entries in memory
indexCacheAll = false
# Precursor m/z tolerance
indexRetrievalMzTolerance = 3.0
# Whether to use average mass instead of monoisotopic mass
indexRetrievalUseAverage = false
# Expected cysteine modification: "CAM" = carbamidomethyl, "ICAT_cl" = cleavable ICAT, "ICAT_uc" = uncleavable ICAT
# Spectra of peptide ions of a different kind of cysteine modification will be ignored
expectedCysteineMod =
# Output file format: pepXML or xml (pepXML format), txt (fixed-width text), or xls (tab-delimited text)
outputExtension = pep.xml
# Output directory: where to put the output files. Defaults to the same directory as the search data file.
outputDirectory = ""
# Detect homologous/identical hits to the top hit up to this specified rank
detectHomologs = 4
# Whether to ignore library spectra of peptide ions with an unmodified cysteine
ignoreSpectraWithUnmodCysteine = false
# Whether to ignore all +1 library spectra
ignoreChargeOneLibSpectra = false
# Whether to ignore abnormal (with Status other than "Normal") spectra
ignoreAbnormalSpectra = false
# Top hits will only be displayed if its F-value is greater than this specified value
hitListTopHitFvalThreshold = 0.0
# Lower hits will only be displayed if its F-value is greater than this specified value
hitListLowerHitsFvalThreshold = 0.45
# Regardless of F-value, homologous/identical lower hits to the top hit will be displayed
hitListShowHomologs = true
# Do not display lower hits no matter what
hitListOnlyTopHit = true
# Do not display the query if it is not searched or if even its top hit does not score higher than hitListTopHitFvalThreshold
hitListExcludeNoMatch = true
# Ignore spectra for which there are less than this many "signficant" peaks
filterMinPeakCount = 10
# Remove all but the top X peaks
filterMaxPeaksUsed = 150
# Remove all peaks smaller than 1/X of the most intense peak
filterMaxDynamicRange = 1000.0
# Only peaks with intensity greated than this threshold will be counted as "significant"
filterCountPeakIntensityThreshold = 2.01
# Peaks with intensity smaller than this threshold will be deleted
filterRemovePeakIntensityThreshold = 2.01
# Ignore spectra for which almost all intensities are below this specified m/z value
filterAllPeaksBelowMz = 520
# Ignore spectra for which all peaks are below this specified intensity
filterMaxIntensityBelow = 0.0
# Dominant peaks (with intensity greater than this fraction of the total intensity) near 515.3Th are deleted
# Set to 0.3 for cleavable ICAT datasets - an impurity peak at 515.3Th is common for these datasets.
filterRemoveHuge515Threshold = 0.0
# Scaling power for raw intensities
peakScalingMzPower = 0.0
peakScalingIntensityPower = 0.5
# Penalty for unassigned peaks
peakScalingUnassignedPeaks = 1.0
# Binning
peakBinningNumBinsPerMzUnit = 1
peakBinningFractionToNeighbor = 0.5
#################################################
