From SPCTools
### COMMON OPTIONS ##############################
### GENERAL ###
# Output file name (without the extension)
outputFileName = /destination/directory/myLibrary
### PEPXML ###
# Set the minimum probability for an identification to be imported into library
minimumProbabilityToInclude = 0.9
# Dataset identifier
datasetName =
### LIBRARY MANIPULATION ###
# Filtering library by criteria
filterCriteria =
# Use probability table to filter library (and modify probabilities)
useProbTable =
# Use protein list to filter library
useProteinList =
# Print MRM transition table
printMRMTable =
# Combining multiple libraries. Choices are UNION, INTERSECT, SUBTRACT and SUBTRACT_HOMOLOG
combineAction = UNION
# Building libraries. Choices are CONSENSUS, BEST_REPLICATE. If not specified, all library
# entries will be left as is.
buildAction =
# Refresh protein mappings against FASTA file specified
refreshDatabase =
# Whether to delete entries with unmapped peptide during refreshing
refreshDeleteUnmapped = false
# Whether to delete entries with multimapped peptide during refreshing
refreshDeleteMultimapped = false
### CONSENSUS ###
# The minimum number of replicates for a peptide ion to be included in library
minimumNumReplicates = 1
### QUALITY FILTER ###
# The quality level for removing spectra from the library
qualityLevelRemove = 2
# The quality level for marking spectra in the library
qualityLevelMark = 5
### DECOY ###
# Whether or not to concatenate real and decoy libraries
decoyConcatenate = false
# The (decoy /real) size ratio
decoySizeRatio = 1
### SEMI-EMPIRICAL SPECTRA ###
# Set(s) of allowable modification tokens to generate semi-empirical spectra
allowableModTokens =
### ADVANCED OPTIONS ############################
### GENERAL ###
# Insert a remark in the comment for each library entry created
remark =
# Whether or not to re-annotate peaks in library entries even if annotations are already present
annotatePeaks = true
# Whether or not to use binary format for library created
binaryFormat = true
# Write all library spectra as .dta or .mgf files
# (e.g. for sequence-searching them)
writeDtaFiles = false
writeMgfFiles = false
### PEPXML ###
# Set the minimum number of amino acids in identification to be included
minimumNumAAToInclude = 6
# Whether to force all N in NXS/T motif to be deamidated (glyco-capture datasets)
setDeamidatedNXST = false
# Whether to add mzXML file to the datasetName (e.g. to distinguish between fractions)
addMzXMLFileToDatabaseName = false
# Set the minimum number of peaks for a spectrum to be included
minimumNumPeaksToInclude = 10
# Set the minimum SEQUEST deltaCn value for a spectrum to be included
minimumDeltaCnToInclude = 0.0
# Absolute noise filter. Remove noise peaks with intensity below this value.
rawSpectraNoiseThreshold = 0.0
# Relative noise filter. Remove noise peaks with intensity below the max intensity divided by this value.
rawSpectraMaxDynamicRange = 100000.0
# Whether or not to centroid peaks. Mostly for Q-TOF spectra in profile mode.
centroidPeaks = false
# Override fragmentation type
setFragmentation =
### LIBRARY MANIPULATION ###
# Whether or not to plot library spectra.
plotSpectra =
### CONSENSUS ###
# Peak quorum, the minimum fraction of replicates containing a peak for that peak to be
# included in the consensus
peakQuorum = 0.6
# Maximum number of peaks used in each replicate in consensus creation
maximumNumPeaksUsed = 300
# Maximum number of peaks kept in the consensus spectra
maximumNumPeaksKept = 150
# Maximum number of replicates used in consensus creation
maximumNumReplicates = 100
# Whether or not to remove dissimilar replicates from consensus building
removeDissimilarReplicates = true
# The type of weights to use to average peak intensities and rank replicates
# Choices are SN (signal-to-noise), XCORR (SEQUEST Xcorr), PROB (probability)
replicateWeight = SN
### QUALITY FILTER ###
# Whether or not to penalize singletons in quality filters
qualityPenalizeSingletons = false
# A probability threshold above which library entries are made immune to quality filters
qualityImmuneProbThreshold = 1.01
# Whether or not to grant immunity to library entries identified with multiple search engines
qualityImmuneMultipleEngines = true
#################################################
