Spectrast create.params

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Revision as of 08:37, 15 January 2010 Henrylam (Talk | contribs) ← Previous diff		Current revision Henrylam (Talk | contribs)
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	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

---

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