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Current by Louis Felix Nothias
on May 07, 2018 15:09.

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h1. Data Analysis
h2. Molecular Networking

{color:#ff0000}[Online Video Tutorials |https://www.youtube.com/channel/UCufTdDIUPjfoN604Igv_29g/videos]{color}
{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 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], and the resources below.


h3. Setup and Running Molecular Networking Workflow

h3. Molecular Networking
h4. Molecular Networking Options

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

See 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], and the resources below.
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]


h4. Setup and Running Molecular Networking Workflow

[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,|https://github.com/mzmine/mzmine2/releases] [OpenMS|https://www.openms.de/], [MS-DIAL|http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/], [MetaboScape|https://www.bruker.com/products/mass-spectrometry-and-separations/ms-software/metaboscape/overview.html]). 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]




h4. Metadata Format

[Molecular Networking Metadata Format |Metadata table in GNPS]




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




[Molecular Networking Group Attribute Formats (Legacy) |Molecular Networking Group Attribute Files]




h2. Data Analysis

h4. Molecular Networking ProteoSAFe Analysis on GNPS (online)

[Molecular Networking Online Analysis|Molecular Networking Analysis Documentation]




h4. Molecular Networking ProteoSAFe Analysis on GNPS (online)

[Molecular Networking Online Analysis|Molecular Networking Analysis Documentation]




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

[Cytoscape 3.6.X Visualization and Analysis Documentation (Recommended)|Public:Cytoscape 3.6.1 Visualization and Analysis Documentation]




[Cytoscape 3.4.X Visualization and Analysis Documentation|Public:Cytoscape 3.4 Visualization and Analysis Documentation]


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


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




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]




h4. Rarefaction Curve Analysis

[Rarefaction Curve Documentation|Rarefaction Curve Documentation]




h3. Dereplication (Library Search)

[Dereplication Documentation|Dereplication Documentation]




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




h2. Insilico Peptidic Natural Products Dereplicator

[Insilico Peptidic Natural Products Dereplicator Documentation]




[Cytoscape 3.4.X Visualization and Analysis Documentation|https://bix-lab.ucsd.edu/display/Public/Cytoscape+3.4+Visualization+and+Analysis+Documentation]




h4. Rarefaction Curve Analysis
[Insilico Peptidic Natural Products Dereplicator Evaluation|https://bix-lab.ucsd.edu/display/Public/Insilico+Peptidic+Natural+Products+Dereplicator+Evaluation+of+GNPS+Massive+datasets]


[Rarefaction Curve Documentation|Rarefaction Curve Documentation]




h3. Dereplication (Library Search)

[Dereplication Documentation|Dereplication Documentation]




h1. Social Networking


h3. Knowledge Base Curation

h4. Library Contribution

[Public:Spectral Library Quality Levels]




h2. Insilico Peptidic Natural Products Dereplicator

[Insilico Peptidic Natural Products Dereplicator Documentation]




[Add Spectra Single Documentation]

[Insilico Peptidic Natural Products Dereplicator Evaluation|https://bix-lab.ucsd.edu/display/Public/Insilico+Peptidic+Natural+Products+Dereplicator+Evaluation+of+GNPS+Massive+datasets]




h1. Social Networking


h3. Knowledge Base Curation

h4. Library Contribution

[Public:Spectral Library Quality Levels]




[Add Batch Spectra Documentation]




[Add Spectra Single Documentation]




h4. Library Curation

[Spectral Library Curation]




[Add Batch Spectra Documentation]




h4. Library Curation

[Spectral Library Curation]

[Public:Challenge Spectra]




[Public:Challenge Spectra]




h2. MassIVE Datsets

[Public:GNPS MassIVE Dataset Creation]




h2. MassIVE Datsets

[Public:GNPS MassIVE Dataset Creation]




[Public:MassIVE Datasets Social Networking]




[Public:MassIVE Datasets Social Networking]











h2. Continuous Identification















[GNPS Molecule Explorer|Public:Molecule Explorer]















h3. My GNPS















h1. Resources















[Public:GNPS API]















[Public:GNPS Workshop, Generation of Molecular Networks in 15 minutes]



[Experimental workflow - GNPS Trinity|https://bix-lab.ucsd.edu/display/Public/GNPS+Trinity+workflow]




[Experimental workflow - GNPS Trinity (Legacy)|https://bix-lab.ucsd.edu/display/Public/GNPS+Trinity+workflow]




























h4. Data Conversion to GNPS Compatible Formats - .mzXML or .mzML

[Data Conversion to GNPS Compatible Formats|https://bix-lab.ucsd.edu/display/Public/Data+Conversion+to+GNPS+Compatible+Formats+-+.mzXML+and+.mzML]













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