Next Steps & Advanced Usage

Running Multiple Jobs

GNPS Local supports multiple simultaneous jobs — just submit them from the web UI. Jobs run in background threads and do not block each other. Be aware that large jobs will compete for CPU resources.

Exporting for External Analysis

Cytoscape (.graphml): Visualize and style the molecular network. The Cytoscape GNPS plugin (available in the Cytoscape App Store) can apply pre-built GNPS visual styles.
R/Python (.tsv files): clusterinfo_summary_enriched.tsv and librarysearch_results_db.tsv are standard tab-separated tables readable by any statistics tool.
Excel: All .tsv output files open directly in Excel via File → Open.

Checklist Before Analyzing Your Own Data

Feature table exported from your software in the correct format (see Section 9)
Feature table and MGF from the same software run (scan numbers must match)
Metadata filename column exactly matches feature table sample names
Single merged MGF file (not one file per sample)
GNPS spectral library .mgf file(s) placed in:
- Windows WSL2: /mnt/d/GNPS_Local/libraries/
- macOS: ~/GNPS_Local/libraries/

Spectral Libraries

Download updated GNPS spectral libraries from:

https://gnps-external.ucsd.edu/gnpslibrary

Place any downloaded .mgf files directly into:

Windows WSL2:

/mnt/d/GNPS_Local/libraries/

macOS:

~/GNPS_Local/libraries/

The library is loaded automatically for every job.

What Is Not Yet Implemented

The following features from cloud GNPS are not yet available locally:

Dereplicator+ (peptidic natural product annotation)
QIIME2 beta-diversity / PCoA statistics
ili 3D spatial mapping
MassIVE dataset search
Automatic method descriptions

These may be added in future versions.