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SpecLibSearcher

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

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.
precursor_mass_tolerance
Precursor mass tolerance, (Th)
round_precursor_to_integer
many precursor m/z multipling number lead to the same number; are packed in the same vector for faster search.Should be higher for high-resolution data
compare_function
function for similarity comparisson
top_hits
save the first <number> top hits. For all type -1
fixed_modifications
fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
variable_modifications
variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
remove_peaks_below_threshold
All peaks of a query spectrum with intensities below <threshold> will be zeroed.
min_peaks
required mininum 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

Input Ports

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

Output Ports

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

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