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GNPS specifications


Unique identifier OMICS_14330
Alternative name Global Natural Products Social Molecular Networking
Restrictions to use None
Community driven Yes
Data access Browse
User data submission Not allowed
Maintained Yes


  • person_outline Pieter Dorrestein

Publication for Global Natural Products Social Molecular Networking

GNPS citations


Experimental Chagas disease induced perturbations of the fecal microbiome and metabolome

PLoS Negl Trop Dis
PMCID: 5864088
PMID: 29529084
DOI: 10.1371/journal.pntd.0006344

[…] ) was performed on the normalized data with our in-house tool ClusterApp using the Bray-Curtis-Faith dissimilarity metric [, ], and visualized in EMPeror []. Molecular networking was performed on the Global Natural Products Social Molecular Networking platform (GNPS) [], with the following parameters: parent mass tolerance 0.02 Da, MS/MS fragment ion tolerance 0.02 Da, cosine score 0.6 or greater, […]


Elucidation of complexity and prediction of interactions in microbial communities

PMCID: 5658597
PMID: 28925555
DOI: 10.1111/1751-7915.12855

[…] n untargeted metabolomics experiment can currently be annotated (Silva et al., ).Improved tools to annotate and integrate metabolomics data sets have been recently developed. One of them is the GNPS (Global Natural Products Social Molecular Networking) that similar to BLAST (Basic Local Alignment Search Tool) for nucleotides and amino acid sequences, assists the storage, analysis and dissemination […]


The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

J Cheminform
PMCID: 5461230
DOI: 10.1186/s13321-017-0220-4
call_split See protocol

[…] of a recently developed Parallel Formula Generator (PFG) [] (Table ). As inputs, we used two sets of 10,000 small (<500 Da) and 20 large (>1500 and <3500 Da) molecular mass values downloaded from the Global Natural Products Social Molecular Networking database []. The mass tolerance was set to 0.001 or 0.01 Da. The CDK v2.0’s Round-Robin formula generator outperformed the other methods in all case […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] ion chromatogram; EssOilDB: Essential Oil Database; EXIMS: Exploring Imaging Mass Spectrometry Data; FT: Fourier transform; FunRich: Functional Enrichment Analysis Tool; GC: gas chromatography; GNPS: Global Natural Products Social Molecular Networking; GUI: graphical user interface; HCS: hierarchical cluster analysis; HMDB: Human Metabolome Database; HRMS: high-resolution mass spectrometry; ICT: I […]


The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

PMCID: 5640684
PMID: 29062930
DOI: 10.1016/j.synbio.2015.12.002

[…] y generated fragments of known secondary metabolites (e.g., those extracted from NORINE or PubChem). Recently, iSNAP has also been extended to identify PK compounds and analogs of known molecules.The Global Natural Products Social Molecular Networking system (GNPS) provides workflows for automated spectra deconvolution, molecular networking to identify compound families and dereplication against a […]


Open Access Metabolomics Databases for Natural Product Research: Present Capabilities and Future Potential

Front Bioeng Biotechnol
PMCID: 4349186
PMID: 25789275
DOI: 10.3389/fbioe.2015.00022

[…] pect is that spectral records are annotated with taxonomic information about the species from which a particular metabolite has been extracted and to which structural class the metabolite belongs.The Global Natural Products Social Molecular Networking resource (GNPS; unpublished) is an MS2 database with an emphasis on natural products of all biological origins (Table ). In addition to unique spect […]


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GNPS institution(s)
Computer Science and Engineering, University of California (UC) San Diego, La Jolla, CA, USA; Department of Pediatrics, UC San Diego, La Jolla, CA, USA
GNPS funding source(s)
This work was partially supported by US National Institutes of Health (NIH) grants 5P41GM103484-07, GM094802, AI095125, GM097509, S10RR029121, UL1RR031980, GM085770, U01TW0007401, and U01AI12316-01.

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