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h1. Introduction to GNPS

Global Natural Products Social Molueclar Networking (GNPS) 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.

{color:#000000}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.{color}
{color:#000000}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.{color} [See Molecular Networking Documentation.|../../../../../../../../../display/Public/Molecular+Networking+Documentation]
{color:#000000}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{color}. See ressources below and the [GNPS paper|http://www.nature.com/nbt/journal/v34/n8/full/nbt.3597.html?WT.ec_id=NBT-201608&spMailingID=52025126&spUserID=ODkwMTM2NjI1NQS2&spJobID=981583612&spReportId=OTgxNTgzNjEyS0].

h4. Setup and Running Workflow

h4. Setup and Running Molecular Networking Workflow

[Molecular Networking Documentation]




[Molecular Networking Group Attribute Formats|Molecular Networking Group Attribute Formats]



h4. Molecular Networking ProteoSAFe Analysis

h4. Molecular Networking ProteoSAFe Analysis on GNPS (online)

[Molecular Networking Online Analysis|Molecular Networking Analysis Documentation]



h4. Cytoscape for Visualization and Analysis of Networks

h4. Cytoscape for Visualization and Analysis of Networks (offline)

[Cytoscape 2.8.X Visualization and Analysis Documentation|Cytoscape 2.8.X Visualization and Analysis Documentation]




[Cytoscape 3.2.X Visualization and Analysis Documentation|Cytoscape 3.2.X Visualization and Analysis Documentation]




h4. Rarefaction Curve Analysis



h2. Dereplication (Library Search)

h3. Dereplication (Library Search)

[Dereplication Documentation|Dereplication Documentation]




h2. Insilico Dereplicator




h1. Social Networking




[Add Spectra Single Documentation]




[Add Batch Spectra Documentation]




h4. Library Curation




[Public:Challenge Spectra]




h2. MassIVE Datsets




[Public:MassIVE Datasets Social Networking]




h2. Continuous Identification




[GNPS Molecule Explorer|Public:Molecule Explorer]




h3. My GNPS




h1. Resources




h4. Data Conversion to .mzXML




h4. File Upload Documentation (Drag and Drop/FTP)