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HighResPrecursorMassCorrector

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Corrects the precursor mass and charge determined by the instrument software.

Web Documentation for HighResPrecursorMassCorrector

Options

version
Version of the tool that generated this parameters file.
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)
mz_tolerance
The precursor mass tolerance. Used to determine matching to feature mass traces.
mz_tolerance_unit
Unit of precursor mass tolerance
rt_tolerance
Additional retention time tolerance added to feature boundaries.
max_trace
Maximum isotopic trace considered in matching a precursor to a feature.
believe_charge
Assume precursor charge to be correct.
keep_original
Make a copy of the precursor and MS2 (true) or discard the original (false).
assign_all_matching
Correct a precursor using all matching features (true) or only the nearest (false). Only evaluated if copies are created (feature:keep_original).
mz_tolerance
The precursor mass tolerance to find the closest MS1 peak. (Disable method by setting value to 0.0)
mz_tolerance_unit
Unit of precursor mass tolerance
mz_tolerance
The precursor mass tolerance to find the highest intensity MS1 peak. Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)
mz_tolerance_unit
Unit of precursor mass tolerance

Input Ports

Input file (centroided data) [mzML]
Features used to correct precursor masses. [featureXML,opt.]

Output Ports

Output file [mzML]
Optional CSV output file for results on 'nearest_peak' or 'highest_intensity_peak' algorithm (see corresponding subsection) containing columns: RT, uncorrectedMZ, correctedMZ, deltaMZ. [csv]

Views

HighResPrecursorMassCorrector Std Output
The text sent to standard out during the execution of HighResPrecursorMassCorrector.
HighResPrecursorMassCorrector Error Output
The text sent to standard error during the execution of HighResPrecursorMassCorrector. (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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Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.1
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