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GNPS Tool Index

This is a global tool index for GNPS. Throughout this documentation we have very detailed information for how to use way more tools than we though we'd have, but its a good problem to have!

However, we recognize it might be difficult for people to simply see what all is availble in GNPS as tool and web services. This table is always evolving and hope to make it easier for people to navigate.

Please help us fill in more completely!

GNPS Workflows

Category Workflow GNPS Link Beta Link Documentation Source Code Citation
Networking Molecular Networking Workflow Workflow Documentation Github Citation
Networking Feature-Based Molecular Networking Workflow Workflow Documentation
Networking Merge Polarity Networks Workflow Workflow Documentation
Networking MS2LDA Motif DB Workflow Workflow Documentation Github-ms2lda, Github-ms2ldaviz Citation-ms2lda, Citation-ms2ldaviz
Networking MolNetEnhancer / MetaboDistTree Workflow Workflow Documentation Github-MolNetEnhancer, Github-MetaboDistTrees Citation
Data Analysis MASST Workflow Workflow Documentation --- Citation
Data Analysis MASST by USI Workflow Workflow Documentation --- Citation
Data Analysis Microbiome-Metabolomics Association - mmvec Workflow - Inactive Workflow ---
Annotation Large Scale Library Search Workflow Workflow ---
Annotation Library Search/Molecular Networking GC Workflow Workflow
Annotation Network Annotation Propogation (NAP) Workflow --- Documentation GitHub Citation
Annotation Qemistree Workflow Workflow
Annotation Dereplicator Workflow --- Documentation GitHub Citation
Annotation Dereplicator+ Workflow --- Documentation GitHub Citation
Annotation MetaMiner Workflow --- Documentation GitHub Citation
Annotation MolDiscovery Workflow --- Documentation GitHub Citation
Annotation Sirius --- Workflow
Data Processing MSHub-GC Deconvolution Workflow Workflow
Data Processing OpenMS Feature Detector for FBMN - Future Feature Workflow Workflow ---
Data Processing LC - MZMine2 Workflow Workflow
Data Processing MSMS-Chooser Workflow Workflow Documentation Github Citation
Data Processing ChemProp --- Workflow Documentation --- ---
Data Processing Spec2vec Workflow Workflow --- --- ---
Data Processing MAGI 2 --- Workflow --- --- ---
Data Processing Falcon Clustering Workflow Workflow --- --- ---
Data Processing NP Classifier Batch Workflow Workflow --- --- ---
Data Processing USI to MGF Conversion Workflow Workflow --- --- ---
Data Processing Spectral Library Conversion --- Workflow --- --- ---
Data Processing Retention Time Modeling --- Workflow --- --- ---

GNPS Web Tools

These are web tools that is run by the GNPS team and provides complementary funcationality to GNPS.

Tool Documentation Source Code Citation
ReDU Documentation GitHub Citation
GNPS Structure Server --- ---
GNPS Quickstart/Batch Validator Documentation ---
GNPS Cytoscape Documentation ---
GNPS MASST Documentation TODO Citation
Metabolomics Spectrum Resolver Documentation GitHub Citation
GNPS2 Networking URL Formatter --- ---
GNPS Mass Spec Calculator --- ---
GNPS Usage Stats Dashboard --- GitHub ---
GNPS2 Classical Networking Upset Plot Dashboard --- GitHub ---
GNPS FBMN Upset Plot Dashboard --- ---
NP Classifier --- GitHub ---
GNPS LCMS Explorer Documentation ---
GNPS Mass Defect Dashboard (Beta) --- ---
GNPS Plotter Dashboard (Beta) --- ---
GNPS Dataset File Explorer (Beta) --- ---
GNPS Public Libraries Download List --- ---
GNPS Public Data Index --- ---
GNPS Spectral Similarity Hub --- ---
Nature Journals Author Quick Entry --- ---
Pubmed Co-Authors List --- ---

GNPS Deprecated Web Tools

Tool Documentation Source Code Citation
GNPS Library Dash Explorer --- ---
GNPS Task Esquisse Server (Beta) --- ---
GNPS Result View Esquisse Server (Super Beta) --- ---
GNPS Text Esquisse Server (Super Beta) --- ---
Qemistree Dashboard Documentation --- ---

GNPS Jupyter Notebooks

These are Jupyter Notebooks that interact with GNPS web resources and do further processing. They serve as a prototype for future built-in infrastructure, check it out!

Tool Documentation Source Code Binder Launch
GNPS MASST Post Processing --- GitHub Binder
GNPS Bioactive Molecular Networks --- GitHub Binder

Community Tools GNPS Interfaces with

Tool Publication
MS2LDA.org Citation
NPAtlas Citation
MIBiG Citation
ClassyFire Citation
SMART NMR Citation
MassBank Citation
Cytoscape Citation
ProteoWizard Citation
SNAP-MS Citation and Documentation

GNPS Tools Interoperability Graph

graph LR
    InputGCData(GC Mass Spectrometry Data) --> MSHUB[GNPS - MSHub Devonvolution]
    Massive --> InputGCData(GC Mass Spectrometry Data)
    Metabolights --> InputGCData(GC Mass Spectrometry Data)
    MSHUB --> GCLibrary[GNPS - GC Library Search and Networking]
    GCLibrary --> Qiime2PCOA
    InputLCData(LC MS/MS Vendor Mass Spectrometry Data) --> MSConvert[MSConvert]
    InputLCData --> Quickstart[GNPS - Quickstart]
    Quickstart --> OpenFormats(Open mzML Format)
    MSConvert --> OpenFormats
    Massive(MassIVE Public Data) --> InputLCData
    Metabolights(Metabolights Public Data) --> InputLCData
    PrivateData(Private MS Data) --> InputLCData
    PrivateData --> InputGCData
    OpenFormats --> GNPSDashboard
    Massive --> GNPSDashboard
    Metabolights --> GNPSDashboard
    Massive --> FBMN
    Massive --> ClassicalNetworking
    OpenFormats --> Dereplicator[GNPS - Dereplicator]
    OpenFormats --> Dereplicator+[GNPS - Dereplicator+]
    OpenFormats --> LibrarySearch(GNPS - Spectral Library Search)
    OpenFormats --> MSMS-Chooser(GNPS - MSMS-Chooser) --> LibraryBatch[GNPS - Batch Library Addition] 
    LibraryBatch --> GNPSLibrary[GNPS - Public Spectral Librarires]
    OpenFormats --> LibrarySingle[GNPS - Single Library Addition] --> GNPSLibrary
    OpenFormats --> GNPSLibrary(GNPS - Public Spectral Libraries)
    OpenFormats --> LibraryBatch --> GNPSLibrary
    OpenFormats --> ClassicalNetworking[GNPS - Classical Molecular Networking]
    OpenFormats --> MZmine2[MZmine2 Feature Finding] --> FBMN
    OpenFormats --> OpenMS[OpenMS Feature Finding] --> FBMN
    OpenFormats --> XCMS[XCMS Feature Finding] --> FBMN
    OpenFormats --> MSDial[MSDial Feature Finding] --> FBMN
    OpenFormats --> GNPSMZmine2[GNPS - MZmine2 Feature Finding] --> FBMN
    MZmine2 --> FBMN[GNPS - Feature Based Molecular Networking]
    ClassicalNetworking --> MS2LDA[GNPS - MS2LDA Substructure Discovery]
    MS2LDA --> MS2LDAORG[MS2LDA.org Motif Exploration]
    ClassicalNetworking --> Qiime2PCOA[Qiime2 PCoA]
    ClassicalNetworking --> Cytoscape[Cytoscape Visualization]
    FBMN --> MS2LDA
    FBMN --> Cytoscape
    FBMN --> Qemistree
    FBMN --> Sirius
    FBMN  --> NAP
    FBMN --> Qiime2PCOA
    ClassicalNetworking  --> NAP[GNPS - Network Annotation Propogation]
    ClassicalNetworking --> MolNetEnhancer --> Cytoscape
    FBMN --> MolNetEnhancer[GNPS - MolNetEnhancer/MetaboDistTree]
    FBMN --> MergePolarity
    FBMN --> Esquisse[GNPS - Interactive Plotting with Esquisse]
    ClassicalNetworking --> MergePolarity[GNPS - Merge Network Polarity]
    Qemistree --> QemistreeDashboard(GNPS - Qemistree Interactive Dashboard)
    GNPSDashboard --> GNPSMZmine2
    GNPSDashboard --> ClassicalNetworking
    FBMN --> GNPSDashboard
    ClassicalNetworking --> GNPSDashboard
    MSHUB --> GNPSDashboard
    GCLibrary --> GNPSDashboard
    Quickstart --> GNPSDashboard
    GNPSDashboard --> MetabolomicsUSI
    GNPSLibrary --> GNPSLibraryExporter
    FBMN --> Dereplicator[GNPS - Dereplicator]
    FBMN --> Dereplicator+[GNPS - Dereplicator+]

    FBMN --> MASST
    ClassicalNetworking --> MASST
    GNPSDashboard --> MASST
    OpenFormats --> MASST

    FBMN --> ChemProp

    OpenFormats --> Sirius

    style GNPSDashboard fill:pink
    style MetabolomicsUSI fill:pink
    style MS2LDAORG fill:pink
    style Qiime2PCOA fill:pink
    style QemistreeDashboard fill:pink
    style Esquisse fill:pink
    style Cytoscape fill:pink
    style GNPSLibraryExporter fill:pink

    style InputGCData fill:lightblue
    style InputLCData fill:lightblue
    style OpenFormats fill:lightblue

    style Massive fill:lightgrey
    style Metabolights fill:lightgrey
    style PrivateData fill:lightgrey

Page Contributors

Ming Wang (91.18%), alan-jarmusch (5.88%), liucaomics (1.96%), Madeleine Ernst (0.98%)

Last update: March 3, 2023 22:38:31