SpecLibSearcher

Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.

Web Documentation for SpecLibSearcher

Options

version
Version of the tool that generated this parameters file.
compare_function
function for similarity comparison
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
mass_tolerance
Width of precursor mass tolerance window
mass_tolerance_unit
Unit of precursor mass tolerance.
min_charge
Minimum precursor charge to be considered.
max_charge
Maximum precursor charge to be considered.
isotopes
Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak)
mass_tolerance
Fragment mass tolerance
top_hits
Maximum number of top scoring hits per spectrum that are reported.
remove_peaks_below_threshold
All peaks of a query spectrum with intensities below <threshold> will be zeroed.
min_peaks
required minimum number of peaks for a query spectrum
max_peaks
Use only the top <number> of peaks.
cut_peaks_below
Remove all peaks which are lower than 1/<number> of the highest peaks. Default equals all peaks which are lower than 0.001 of the maximum intensity peak
fixed
Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'
variable
Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'
variable_max_per_peptide
Maximum number of residues carrying a variable modification per candidate peptide

Input Ports

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Input files [mzML]
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searchable spectral library (MSP format) [msp]

Output Ports

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Output files. Have to be as many as input files [idXML]

Views

SpecLibSearcher Std Output
The text sent to standard out during the execution of SpecLibSearcher.
SpecLibSearcher Error Output
The text sent to standard error during the execution of SpecLibSearcher. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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Further Links

Developers

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