SiriusExport

Metabolite identification using single and tandem mass spectrometry

Options

version: Version of the tool that generated this parameters file.
filter_by_num_masstraces: Number of mass traces each feature has to have to be included. To use this parameter, setting the feature_only flag is necessary
precursor_mz_tolerance: Tolerance window for precursor selection (Feature selection in regard to the precursor)
precursor_mz_tolerance_unit: Unit of the preprocessing_precursor_mz_tolerance
precursor_rt_tolerance: Tolerance window (left and right) for precursor selection [seconds]
isotope_pattern_iterations: Number of iterations that should be performed to extract the C13 isotope pattern. If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns
feature_only: Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature
no_masstrace_info_isotope_pattern: Set to true if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead
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)

: Internal SIRIUS .ms format after OpenMS preprocessing [ms]
: File (.tsv) with information on processed compounds which are associated with a feature. Required for AssayGeneratorMetaboSirius tool. [tsv]

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

v5.3

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: 3.2.0.202409181756

On NodePit since: 2024-10-17

Last update: 2024-10-22

KNIME versions: Since v5.3

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