IconSimpleSearchEngine0 ×

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

Annotates MS/MS spectra using SimpleSearchEngine.

Web Documentation for SimpleSearchEngine

Options

version
Version of the tool that generated this parameters file.
enzyme
The enzyme used for peptide digestion.
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)
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
mass_tolerance_unit
Unit of fragment m
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
min_size
Minimum size a peptide must have after digestion to be considered in the search.
max_size
Maximum size a peptide must have after digestion to be considered in the search (0 = disabled).
missed_cleavages
Number of missed cleavages.
top_hits
Maximum number of top scoring hits per spectrum that are reported.

Input Ports

input file [mzML]
input file [fasta]

Output Ports

output file [idXML]

Views

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

Update Site

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

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