GNPS data

NPLinker requires GNPS molecular networking data as input. It currently accepts data from the following GNPS workflows:

• METABOLOMICS-SNETS (data should be downloaded from the option Download Clustered Spectra as MGF)
• METABOLOMICS-SNETS-V2 (Download Clustered Spectra as MGF)
• FEATURE-BASED-MOLECULAR-NETWORKING (Download Cytoscape Data)

Mappings from GNPS data to NPLinker input

METABOLOMICS-SNETS workflowMETABOLOMICS-SNETS-V2FEATURE-BASED-MOLECULAR-NETWORKING

NPLinker input	GNPS file in the archive of Download Clustered Spectra as MGF
spectra.mgf	METABOLOMICS-SNETS*.mgf
molecular_families.tsv	networkedges_selfloop/*.pairsinfo
annotations.tsv	result_specnets_DB/*.tsv
file_mappings.tsv	clusterinfosummarygroup_attributes_withIDs_withcomponentID/*.tsv

For example, the file METABOLOMICS-SNETS*.mgf from the downloaded zip archive is used as the spectra.mgf input file of NPLinker.

When manually preparing GNPS data for NPLinker, the METABOLOMICS-SNETS*.mgf must be renamed to spectra.mgf and placed in the gnps sub-directory of the NPLinker working directory.

NPLinker input	GNPS file in the archive of Download Clustered Spectra as MGF
spectra.mgf	METABOLOMICS-SNETS-V2*.mgf
molecular_families.tsv	networkedges_selfloop/*.selfloop
annotations.tsv	result_specnets_DB/*.tsv
file_mappings.tsv	clusterinfosummarygroup_attributes_withIDs_withcomponentID/*.clustersummary

NPLinker input	GNPS file in the archive of Download Cytoscape Data
spectra.mgf	spectra/*.mgf
molecular_families.tsv	networkedges_selfloop/*.selfloop
annotations.tsv	DB_result/*.tsv
file_mappings.csv	quantification_table/*.csv

Note that file_mappings.csv is a CSV file, not a TSV file, different from the other workflows.