Added by Mingxun Wang, last edited by Louis Felix Nothias on Jul 22, 2017  (view change)


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Introduction to GNPS

Global Natural Products Social Molecular Networking (GNPS) web-platform provides public data set deposition and/or retrieval through the Mass Spectrometry Interactive Virtual Environment (MassIVE) data repository. The GNPS analysis infrastructure further enables online dereplication, automated molecular networking analysis, and crowdsourced MS/MS spectrum curation. Each data set added to the GNPS repository is automatically reanalyzed in the next monthly cycle of continuous identification.

For more information, please check out the GNPS paper published in Nature Biotechnology by Ming et al , as well as the video and the ressource sections below.

Data Analysis

Online Video Tutorials

Molecular Networking

Molecular networks are visual displays of the chemical space present in tandem mass spectrometry (MS/MS) experiments. This visualization approach can detect sets of spectra from related molecules (so-called spectral networks), even when the spectra themselves are not matched to any known compounds.
The visualization of molecular networks in GNPS represents each MS/MS spectrum as a node, and spectrum-to-spectrum relatedness as edges (connections) between nodes.

See the GNPS paper, and the resources below.

Setup and Running Molecular Networking Workflow

Molecular Networking Documentation

Molecular Networking Group Attribute Formats

Molecular Networking ProteoSAFe Analysis on GNPS (online)

Molecular Networking Online Analysis

Cytoscape for Visualization and Analysis of Networks (offline)

Cytoscape 2.8.X Visualization and Analysis Documentation

Cytoscape 3.2.X Visualization and Analysis Documentation

Cytoscape 3.4.X Visualization and Analysis Documentation

Rarefaction Curve Analysis

Rarefaction Curve Documentation

Dereplication (Library Search)

Dereplication Documentation

Insilico Peptidic Natural Products Dereplicator

Insilico Peptidic Natural Products Dereplicator Documentation

Insilico Peptidic Natural Products Dereplicator Evaluation

Social Networking

Knowledge Base Curation

Library Contribution

Spectral Library Quality Levels

Add Spectra Single Documentation

Add Batch Spectra Documentation

Library Curation

Spectral Library Curation

Challenge Spectra

MassIVE Datsets

GNPS MassIVE Dataset Creation

MassIVE Datasets Social Networking

Continuous Identification

GNPS Continuous Identification and Data Exploration

GNPS Molecule Explorer


User Summary Page




GNPS Workshop, Generation of Molecular Networks in 15 minutes

Experimental workflow - GNPS Trinity

Data Conversion to .mzXML

Data Conversion to .mzXML

File Upload Documentation (Drag and Drop/FTP)

Input File Uploads