HighResPrecursorMassCorrector

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

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: Overrides 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

: 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]

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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To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.0.0.202307112039

On NodePit since: 2023-12-06

Last update: 2024-04-22

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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