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 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.
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:
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:
Add Spectra Single Documentation
Cytoscape 2.8.X Visualization and Analysis Documentation
Data Conversion to GNPS Compatible Formats - .mzXML and .mzML
GNPS Continuous Identification and Data Exploration
GNPS MassIVE Dataset Creation
Input File Uploads
Insilico Peptidic Natural Products Dereplicator Documentation
MassIVE Datasets Social Networking
Molecular Networking Analysis Documentation
Molecular Networking Documentation
Molecular Networking Group Attribute Files
NIH Natural Products Spectral Library NPAC ACONN
Rarefaction Curve Documentation
Spectral Library Curation
Spectral Library Quality Levels
User Summary Page