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

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.)

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