Spectrast create.params

From SPCTools

---

Revision as of 21:16, 22 June 2007

### 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 =

# 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 =

### 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



### ADVANCED OPTIONS ############################

### GENERAL ###

# Insert a remark in the comment for each library entry created
remark = 

# Whether or not to annotate peaks in library entries
annotatePeaks = true;

# Whether or not to use binary format for library created
binaryFormat = true;

# Whether or not to write all library spectra as .dta files
# (e.g. for sequence-searching them)
writeDtaFiles = false;

### PEPXML ###
    
# Noise threshold for raw spectra. All peaks below threshold will be removed
rawSpectraNoiseThreshold = 0.0;

# Set N in NX(S/T) motif to be deamidated; N not in NX(S/T) motif to be unmodified
# For glyco-capture methods
setDeamidatedNXST = false;

# Set the minimum deltaCn (SEQUEST) for an identification to be imported into library 
minimumDeltaCnToInclude = 0.0;

### 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 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

# The maximum number of peaks kept for singleton entries
denoiseSingles = 150

  
### 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;
  
#################################################