https://github.com/merlin-ms/awesome-mass-spectral-libraries

https://github.com/merlin-ms/awesome-mass-spectral-libraries

List: awesome-mass-spectral-libraries

Last synced: 17 days ago
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• Host: GitHub
• URL: https://github.com/merlin-ms/awesome-mass-spectral-libraries
• Owner: merlin-ms
• License: cc0-1.0
• Created: 2024-05-06T17:29:12.000Z (8 months ago)
• Default Branch: main
• Last Pushed: 2024-05-07T07:52:00.000Z (8 months ago)
• Last Synced: 2024-10-15T22:01:20.031Z (3 months ago)
• Size: 11.7 KB
• Stars: 12
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md
  • Contributing: contributing.md
  • License: LICENSE
  • Code of conduct: code-of-conduct.md

Awesome Lists containing this project

• awesome-mass-spectrometry-ml - Awsome Mass Spectra Libraries

README

        
# Awesome Mass Spectral Libraries [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)

> A curated list of resources and tools to use and build mass spectral libraries.

## Contents

- [Specifications](#specifications)

- [Spectral Libraries](#spectral-libraries)

- [Quality Assessment](#spectral-quality-assessment)

- [Library Generation](#spectral-library-generation)

- [Handling of Spectral Libraries](#handling-of-spectral-libraries)

- [Compound Annotation](#compound-annotation)

- [Other Related Resources](#other-related-resources)

## Specifications

- [mzSpecLib](https://github.com/HUPO-PSI/mzSpecLib): MS library format specifications

## Spectral Libraries

### Public (Open)

- [GNPS](https://gnps-external.ucsd.edu/gnpslibrary)

- [MassBankEU](https://massbank.eu/MassBank/), contribute spectra on GitHub

- [MoNA](https://mona.fiehnlab.ucdavis.edu/) (MassBank of North America)

### Commercial

- [NIST](https://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:start#libraries)

- [mzCloud](https://www.mzcloud.org/): MSn spectral tree library

## Spectral Quality Assessment

- [msPurity](https://pubs.acs.org/doi/10.1021/acs.analchem.6b04358): R, purity score 

## Spectral Library Generation

- [mzmine](https://github.com/mzmine/mzmine/): Java, GUI/CLI, process MS data, ion mobility spectrometry, generate spectral libraries, visualize spectra

- [RMassBank](https://github.com/MassBank/RMassBank) + [scripts](https://github.com/meowcat/RMassBank-scripts/): Generate spectral libraries, requires specific data acquisition method

- [MSMS-Chooser](https://ccms-ucsd.github.io/GNPSDocumentation/msmschooser/) - Automatically select MS/MS from LC standard runs and generate GNPS libraries

## Handling of Spectral Libraries

- [Metabolomics USI resolver](https://metabolomics-usi.gnps2.org/): Web-tool, visualize library spectra and mirror plots

## Compound Annotation

- [FASST / fastMASST](https://fasst.gnps2.org/): Search single spectrum against public libraries or studies 

- [GNPS2](https://gnps2.org/): Web-apps, nextflow workflows, spectral library matching, molecular networking

- [mzmine](https://github.com/mzmine/mzmine/): Spectral library matching, molecular networking, MS2Deepscore (soon)

## Other Related Resources

- [RepoRT](https://github.com/michaelwitting/RepoRT) ([cite](https://www.nature.com/articles/s41592-023-02143-z)): Retention time database

## Contribute

Contributions welcome! Read the [contribution guidelines](contributing.md) first.