MRMPairFinder

Util which can be used to evaluate labeled pair ratios on MRM features.

Options

version: Version of the tool that generated this parameters file.
mass_tolerance: Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features.
RT_tolerance: Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file.
RT_pair_tolerance: Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have.
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)

: Input featureXML file containing the features of the MRM experiment spectra. [featureXML]
: Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt [csv]

: Output consensusXML file were the pairs of the features will be written to. [consensusXML]
: Output featureXML file, only written if given, skipped otherwise. [featureXML]

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