Added by Mingxun Wang, last edited by Louis Felix Nothias on May 07, 2018  (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.

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 Options

There are two ways methods to create molecular networks at GNPS.

1) Classic Molecular Networking (Recommended): MS-Cluster will analyze every MS/MS spectra resulting from ions that fall within the defined precursor ion mass tolerance (PIMT), and will merge the nearly-identical MS/MS spectra (above the cosine score) into a single consensus MS/MS spectrum. Each consensus MS/MS spectrum usually consist of multiple MS/MS spectra from across multiple LC-MS runs (or data files). Mass spectrometry data must be in a compatible, universal format (mzXML, mzML or mgf). For a overview of workflow, follow the link:

Molecular Networking Documentation

2) Feature based Molecular Networking (Advanced Users): MS/MS spectra will be organized to a MS1-feature table (containing quantification data) using the feature detection tools (MZmine2, OpenMS, MS-DIAL, MetaboScape). Mass spectrometry data should be uploaded as a condensed MGF file (Information from multiple samples will be contained in one file). For details about this workflow, follow the link:

Feature Based Molecular Networking

Metadata Format

Molecular Networking Metadata Format

Molecular Networking Group Attribute Formats (Legacy)

Data Analysis

Molecular Networking ProteoSAFe Analysis on GNPS (online)

Molecular Networking Online Analysis

Cytoscape for Visualization and Analysis of Networks (offline)

Cytoscape 3.6.X Visualization and Analysis Documentation (Recommended)

Cytoscape 3.4.X Visualization and Analysis Documentation

Cytoscape 3.2.X Visualization and Analysis Documentation

Cytoscape 2.8.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 (Legacy)

Data Conversion to GNPS Compatible Formats - .mzXML or .mzML

Data Conversion to GNPS Compatible Formats

File Upload Documentation (Drag and Drop/FTP)

Input File Uploads