Spectrast create.params
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(Difference between revisions)
| Revision as of 21:16, 22 June 2007 Henrylam (Talk | contribs) (An example spectrast_create.params file) ← Previous diff |
Current revision Henrylam (Talk | contribs) |
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| Line 10: | Line 10: | ||
| # Set the minimum probability for an identification to be imported into library | # Set the minimum probability for an identification to be imported into library | ||
| - | minimumProbabilityToInclude = 0.9; | + | minimumProbabilityToInclude = 0.9 |
| # Dataset identifier | # Dataset identifier | ||
| Line 19: | Line 19: | ||
| # Filtering library by criteria | # Filtering library by criteria | ||
| filterCriteria = | 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 | # Combining multiple libraries. Choices are UNION, INTERSECT, SUBTRACT and SUBTRACT_HOMOLOG | ||
| Line 26: | Line 35: | ||
| # entries will be left as is. | # entries will be left as is. | ||
| buildAction = | 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 ### | ### CONSENSUS ### | ||
| # The minimum number of replicates for a peptide ion to be included in library | # The minimum number of replicates for a peptide ion to be included in library | ||
| - | minimumNumReplicates = 1; | + | minimumNumReplicates = 1 |
| ### QUALITY FILTER ### | ### QUALITY FILTER ### | ||
| Line 40: | Line 58: | ||
| qualityLevelMark = 5 | 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 ############################ | ### ADVANCED OPTIONS ############################ | ||
| Line 49: | Line 78: | ||
| remark = | remark = | ||
| - | # Whether or not to annotate peaks in library entries | + | # Whether or not to re-annotate peaks in library entries even if annotations are already present |
| - | annotatePeaks = true; | + | annotatePeaks = true |
| # Whether or not to use binary format for library created | # Whether or not to use binary format for library created | ||
| - | binaryFormat = true; | + | binaryFormat = true |
| - | # Whether or not to write all library spectra as .dta files | + | # Write all library spectra as .dta or .mgf files |
| # (e.g. for sequence-searching them) | # (e.g. for sequence-searching them) | ||
| - | writeDtaFiles = false; | + | writeDtaFiles = false |
| + | writeMgfFiles = false | ||
| ### PEPXML ### | ### PEPXML ### | ||
| - | # Noise threshold for raw spectra. All peaks below threshold will be removed | + | # Set the minimum number of amino acids in identification to be included |
| - | rawSpectraNoiseThreshold = 0.0; | + | minimumNumAAToInclude = 6 |
| - | # Set N in NX(S/T) motif to be deamidated; N not in NX(S/T) motif to be unmodified | + | # Whether to force all N in NXS/T motif to be deamidated (glyco-capture datasets) |
| - | # For glyco-capture methods | + | setDeamidatedNXST = false |
| - | 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 = | ||
| - | # Set the minimum deltaCn (SEQUEST) for an identification to be imported into library | ||
| - | minimumDeltaCnToInclude = 0.0; | ||
| ### LIBRARY MANIPULATION ### | ### LIBRARY MANIPULATION ### | ||
| Line 84: | Line 132: | ||
| # Maximum number of peaks used in each replicate in consensus creation | # Maximum number of peaks used in each replicate in consensus creation | ||
| maximumNumPeaksUsed = 300 | maximumNumPeaksUsed = 300 | ||
| + | |||
| + | # Maximum number of peaks kept in the consensus spectra | ||
| + | maximumNumPeaksKept = 150 | ||
| # Maximum number of replicates used in consensus creation | # Maximum number of replicates used in consensus creation | ||
| Line 89: | Line 140: | ||
| # Whether or not to remove dissimilar replicates from consensus building | # Whether or not to remove dissimilar replicates from consensus building | ||
| - | removeDissimilarReplicates = true; | + | removeDissimilarReplicates = true |
| # The type of weights to use to average peak intensities and rank replicates | # The type of weights to use to average peak intensities and rank replicates | ||
| # Choices are SN (signal-to-noise), XCORR (SEQUEST Xcorr), PROB (probability) | # Choices are SN (signal-to-noise), XCORR (SEQUEST Xcorr), PROB (probability) | ||
| replicateWeight = SN | replicateWeight = SN | ||
| - | |||
| - | # The maximum number of peaks kept for singleton entries | ||
| - | denoiseSingles = 150 | ||
| Line 102: | Line 150: | ||
| # Whether or not to penalize singletons in quality filters | # Whether or not to penalize singletons in quality filters | ||
| - | qualityPenalizeSingletons = false; | + | qualityPenalizeSingletons = false |
| # A probability threshold above which library entries are made immune to quality filters | # A probability threshold above which library entries are made immune to quality filters | ||
| - | qualityImmuneProbThreshold = 1.01; | + | qualityImmuneProbThreshold = 1.01 |
| # Whether or not to grant immunity to library entries identified with multiple search engines | # Whether or not to grant immunity to library entries identified with multiple search engines | ||
| - | qualityImmuneMultipleEngines = true; | + | qualityImmuneMultipleEngines = true |
| ################################################# | ################################################# | ||
| </nowiki></pre> | </nowiki></pre> | ||
Current revision
### 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
#################################################
