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 Spectral Similarity Hub | --- | --- | --- |
| GNPS2 Tiny Mass Sharer | --- | --- | --- |
| GNPS2 MassQL Visualizer | --- | --- | --- |
| GNPS2 MassQL Analysis/Chatbot | --- | --- | --- |
| GNPS2 USI Playground | --- | --- | --- |
| GNPS2 Network Customization Playground | --- | --- | --- |
| CMMC Batch validation | --- | GitHub | --- |
Web Interfaces Description¶
MS/MS Spectrum Summary App¶
Here is a little app that can take a set of MS/MS spectra and understand the consistent fragmentation.
Molecular Networking Reformatting App¶
This little app can reformat molecular networking outputs to create tall tables to make downstream analysis a bit easier.
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.
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
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.
MassQL Analysis App¶
This app makes working with MassQL a lot easier.
You can do the following:
- Play around with MassQL against MS/MS spectral libraries
- Use an LLM to write and interact with MassQL queries for the first time
- Use an LLM to explain the MassQL Queries
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 |  |
| GNPS2 MassQL and Networking Integration | --- | GitHub | |
| GNPS2 Networking Family Consistent Fragmentation | --- | GitHub | |
| GNPS2 MassQL Post Processing | --- | GitHub | |
| CMMC Integration | --- | GitHub | |
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 |