Spectrast.params
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(Difference between revisions)
| Revision as of 20:53, 22 June 2007 Henrylam (Talk | contribs) (An example spectrast.params file) ← Previous diff |
Current revision Henrylam (Talk | contribs) |
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| # A database file to be included in .pepXML outputs for downstream TPP processing - replace with your own | # A database file to be included in .pepXML outputs for downstream TPP processing - replace with your own | ||
| databaseFile = /path/to/myDatabase.fasta | 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 | # Whether to keep all accessed library entries in memory | ||
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| # Precursor m/z tolerance | # Precursor m/z tolerance | ||
| indexRetrievalMzTolerance = 3.0 | 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 | # Expected cysteine modification: "CAM" = carbamidomethyl, "ICAT_cl" = cleavable ICAT, "ICAT_uc" = uncleavable ICAT | ||
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| # Output file format: pepXML or xml (pepXML format), txt (fixed-width text), or xls (tab-delimited text) | # Output file format: pepXML or xml (pepXML format), txt (fixed-width text), or xls (tab-delimited text) | ||
| - | outputExtension = xml | + | outputExtension = pep.xml |
| - | ### ADVANCED OPTIONS ############################ | + | # Output directory: where to put the output files. Defaults to the same directory as the search data file. |
| - | + | outputDirectory = | |
| - | # 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 = | + | |
| # Detect homologous/identical hits to the top hit up to this specified rank | # Detect homologous/identical hits to the top hit up to this specified rank | ||
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| # Regardless of F-value, homologous/identical lower hits to the top hit will be displayed | # Regardless of F-value, homologous/identical lower hits to the top hit will be displayed | ||
| - | hitListShowHomologs = true; | + | hitListShowHomologs = true |
| # Do not display lower hits no matter what | # Do not display lower hits no matter what | ||
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| hitListExcludeNoMatch = true | hitListExcludeNoMatch = true | ||
| - | # Save all query spectra and matched library spectra as .msp files | + | # Ignore spectra for which there are less than this many "signficant" peaks |
| - | saveSpectra = false | + | filterMinPeakCount = 10 |
| - | # tar-gzipped all the spectra .msp files to save space | + | # Remove all but the top X peaks |
| - | tgzSavedSpectra = false | + | filterMaxPeaksUsed = 150 |
| - | # Ignore spectra for which there are less than this many "signficant" peaks | + | # Remove all peaks smaller than 1/X of the most intense peak |
| - | filterMinPeakCount = 6 | + | filterMaxDynamicRange = 1000.0 |
| # Only peaks with intensity greated than this threshold will be counted as "significant" | # Only peaks with intensity greated than this threshold will be counted as "significant" | ||
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| # Ignore spectra for which almost all intensities are below this specified m/z value | # Ignore spectra for which almost all intensities are below this specified m/z value | ||
| filterAllPeaksBelowMz = 520 | 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 | # Dominant peaks (with intensity greater than this fraction of the total intensity) near 515.3Th are deleted | ||
Current revision
### 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 #################################################
