Spectrast.params

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### 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 

#################################################
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