GNPSExport

Export representative consensus MS/MS scan per consensusElement into a .MGF file format.

See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms

Options

version: Version of the tool that generated this parameters file.
output_type: specificity of mgf output information
peptide_cutoff: Number of most intense peptides to consider per consensus element; '-1' to consider all identifications.
ms2_bin_size: Bin size (Da) for fragment ions when merging ms2 scans.
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)
cos_similarity: Cosine similarity threshold for merged_spectra output.

: Input consensusXML file containing only consensusElements with "peptide" annotations. [consensusXML]
: Original mzml files containing the ms2 spectra (aka peptide annotation). #br#Must be in order that the consensusXML file maps the original mzML files. [mzML]

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

v5.9

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

Plugin version: 3.5.0.202512111229

On NodePit since: 2025-12-12

Last update: 2026-01-13

KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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