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GNPS2 Tool Index

This is a global tool index for GNPS2. Throughout this documentation we have very detailed information for how to use way more tools than we thought we'd have, but it's a good problem to have!

However, we recognize it might be difficult for people to simply see what all is available 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!

GNPS2 Web Tools

These are web tools that is run by the GNPS2 team and provides complementary functionality to GNPS2.

Tool Documentation Source Code Citation
Pubmed Co-Authors List --- --- ---
Nature Journals Author Quick Entry --- --- ---
GNPS2 Spectral Similarity Hub --- --- ---
GNPS2 Structure Server --- --- ---
GNPS2 Cytoscape --- --- ---
Metabolomics Spectrum Resolver Documentation GitHub Citation
GNPS2 Networking URL Formatter --- --- ---
GNPS2 Classical Networking Upset Plot Dashboard --- GitHub ---
GNPS2 FBMN Upset Plot Dashboard --- --- ---
NP Classifier --- GitHub ---
GNPS2 Dashboard --- --- ---
GNPS2 Plotter Dashboard (Beta) --- --- ---
GNPS2 Dataset File Explorer (Beta) --- --- ---
GNPS2 Public Libraries Download List --- --- ---
GNPS2 Tiny Mass Sharer --- --- ---
GNPS2 MassQL Visualizer --- --- ---
GNPS2 MassQL Analysis/Chatbot --- --- ---
GNPS2 USI Playground --- --- ---
GNPS2 Network Customization Playground --- --- ---
FBmnStatsGUIde --- GitHub ---
Chemical Proportionality --- --- ---
CorrOmics --- --- ---
CMMC Batch validation --- GitHub ---
MetaboApp - DrugReadouts --- GitHub ---
MetaboApp - CMMC Dashboard --- GitHub ---
MetaboApp - MassQL Post-MN --- GitHub ---

Web Interfaces Description

MassQL Post-MN

Enables users to perform spectral pattern-based queries directly on post-processed GNPS molecular networking outputs using the MassQL language.

MassQL Post-MN

Drug Readout

Maps chemical features to standardized pharmacological vocabularies to identify drug-derived signals in complex datasets.

Drug Readout

CMMC Dashboard

Visualizes enrichment analyses using the Collaborative Microbial Metabolite Center (CMMC) knowledgebase, linking features to known microbial metabolic products.

CMMC Dashboard

FBMN Stats

Offers statistical analysis tools tailored for Feature-Based Molecular Networking (FBMN) outputs, including differential abundance and multivariate assessments.

FBMN Stats

Chemical Proportionality

Analyzes relative abundance trends of structurally related compounds to infer biochemical transformations or metabolic dependencies.

Chemical Proportionality

CorrOmics

Supports correlation-based multi-omics integration, linking metabolomics features to other data types such as genomics or transcriptomics.

CorrOmics

MS/MS Spectrum Summary App

Here is a little app that can take a set of MS/MS spectra and understand the consistent fragmentation.

Spectrum Summary App

Molecular Networking Reformatting App

This little app can reformat molecular networking outputs to create tall tables to make downstream analysis a bit easier.

Networking Reformatting App

Coauthor Summarizer

This app can take all of your publications and tell you who your coauthors were in the last n years. Pretty useful for NSF proposals.

Coauthor App

TinyMass App

This app is like tinyurl but for mass spectra. You can easily share MS spectra and get a USI that can be used in a ton of different places

TinyMass App

USI Generation App

This app will help to create USIs from a variety of places from datasets to GNPS2 analysis jobs. Making it easier to interact with the rest of the ecosystem.

USI Generation App

MassQL Analysis App

This app makes working with MassQL a lot easier.

You can do the following:

  1. Play around with MassQL against MS/MS spectral libraries
  2. Use an LLM to write and interact with MassQL queries for the first time
  3. Use an LLM to explain the MassQL Queries

MassQL Analysis App

GNPS2 Jupyter Notebooks

These notebooks are for postprocessing of results from GNPS/GNPS2 and other computational processing that have not been integrated yet. If they are super useful, we can integrate into high throughput workflows. For now, give them a try!

Tool Documentation Source Code Binder Launch
GNPS2 MASST Post Processing --- GitHub Binder
GNPS2 MassQL and Networking Integration --- GitHub Binder
GNPS2 Networking Family Consistent Fragmentation --- GitHub Binder
GNPS2 MassQL Post Processing --- GitHub Binder
CMMC Integration --- GitHub Binder

Community Tools GNPS2 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