Rusteomics 1.1 - building a house on the foundations

[douweschulte]

Title

Rusteomics 1.1 - building a house on the foundations

Abstract

Rust is a relatively new programming language known for its impressive performance, robustness, and developer-friendliness. At the EuBIC-MS Developers Meeting 2023, the Rusteomics community was founded to leverage the Rust programming language in mass spectrometry data analysis. At the EuBIC Developers Meeting 2025 we formalized the Rusteomics community around shared values and coding practices, as described in a mission statement, decision making policies, and a code of conduct. Moreover, the code-base was efficiently kickstarted by the donation of the existing rustyms library, and the basis for Python bindings was laid.

The result was an open-source library that could perform many foundational mass spectrometry analysis tasks. By now, the project has been adopted in multiple other software packages and has been used for various research articles. The project is actively developed by a handful of dedicated people who meet online monthly to discuss recent changes and to help each other extend the library.

This hackathon will be focussed on extending the applicability of the Rusteomics library and will be another opportunity for us to learn from each other.

Project Plan

• Extend the applicability of the library by adding additional abilities for example:
  • Internal fragmentation, add more features
  • Extend glycan fragmentation, Z/C or even A/X
  • Add support for other (HUPO-PSI) formats, we think the following could be nice to have support for:
    • PEFF
    • Uniprot XML
    • Uniprot EMBL flat
    • mzQC
    • SDRF
    • WURCS
  • Extend the current code to support other mass spec techniques (small molecules, lipids, RNA, DNA, etc)
  • Add a scoring crate, e.g. with Xcorr and MSAmanda scoring
  • Or any other extension that currently blocks you from using it
• Extend the use of the library by creating better bindings R and/or other languages, we currently have Python bindings but they need some input from Python users.
• Discuss missing features and long term plans

Technical Details

• The main programming language is Rust, but if you want to extend the bindings for your language of choice no prior Rust experience is needed
• We will be using git(+github)
• Affinity to work on large community code bases
• Main code bases:
  • https://github.com/rusteomics/mzcore
  • https://github.com/mobiusklein/mzdata

Contact information

Douwe Schulte
Utrecht University, Utrecht, Netherlands
d.schulte@uu.nl
Dirk Winkelhardt
Ruhr-University Bochum, Medical Faculty, Medical Bioinformatics
dirk.winkelhardt@rub.de
Ralf Gabriels
VIB-UGent Center for Medical Biotechnology, VIB, Belgium; Department of Biomolecular Medicine, Ghent University, Belgium