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GNPS

NPLinker requires GNPS molecular networking data as input. It currently accepts data from both GNPS1 (https://gnps.ucsd.edu) and GNPS2 (https://gnps2.org) workflows.

GNPS1 workflows supported by NPLinker are:

  • 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)

GNPS2 workflows supported by NPLinker are:

  • classical_networking_workflow (Download All Results)
  • feature_based_molecular_networking_workflow (Download All Results)

Mappings from GNPS1 data to NPLinker input

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 GNPS1 workflows.

Mappings from GNPS2 data to NPLinker input

NPLinker input GNPS file in the archive of Download All Results
spectra.mgf nf_output/clustering/specs_ms.mgf
molecular_families.tsv nf_output/networking/filtered_pairs.tsv
annotations.tsv nf_output/library/merged_results_with_gnps.tsv
file_mappings.csv nf_output/clustering/featuretable_reformatted_presence.csv
NPLinker input GNPS file in the archive of Download All Results
spectra.mgf nf_output/clustering/specs_ms.mgf
molecular_families.tsv nf_output/networking/filtered_pairs.tsv
annotations.tsv nf_output/library/merged_results_with_gnps.tsv
file_mappings.csv nf_output/clustering/featuretable_reformated.csv