🦀 Rust: 🐍 Python:

Match those fragments!

A peptide fragmentation matching library for Rust. Built to handle very complex peptides in a sensible way.

Features

• Read ProForma sequences (complete specification supported: 'level 2-ProForma + top-down compliant + cross-linking compliant + glycans compliant + mass spectrum compliant')
• Generate theoretical fragments with control over the fragmentation model from any ProForma peptidoform/proteoform
  • Generate theoretical fragments for chimeric spectra
  • Generate theoretical fragments for cross-links (also disulfides)
  • Generate theoretical fragments for modifications of unknown position
  • Generate peptide backbone (a, b, c, x, y, and z) and satellite ion fragments (w, d, and v)
  • Generate glycan fragments (B, Y, and internal fragments)
• Integrated with mzdata for reading raw data files
• Match spectra to the generated fragments
• Align peptides based on mass
• Fast access to the IMGT database of antibody germlines
• Reading of multiple identified peptide file formats (Fasta, MaxQuant, MSFragger, Novor, OPair, Peaks, and Sage)
• Exhaustively fuzz tested for reliability (using cargo-afl)
• Extensive use of uom for compile time unit checking
• Python bindings are provided to several core components of the rustyms library. Go to the Python documentation for more information.

Folder organisation

rustyms

This is the main library. This contains all source code, databases (Unimod etc) and example data to run the rustyms library.

examples

Some examples on how to use the rustyms library are provided here, see the readme file in the examples themselves for more details.

fuzz

The harness to fuzz test the library for increased stability, see the readme for more details.

rustyms-py

This Rust library provides python bindings (using pyO3) for rustyms.

rustyms-generate-databases

Using the rustyms-generate-databases the definitions for the databases can be updated. See the readme on the download locations for all databases. Then run cargo run -p rustyms-generate-databases (from the root folder of this repository).

rustyms-generate-imgt

Using the rustyms-generate-imgt the definitions for the germlines can be updated. Put the imgt.dat.Z file in the rustyms-generate-imgt/data directory and unpack it (this can be downloaded from https://www.imgt.org/download/LIGM-DB/imgt.dat.Z). Then run cargo run -p rustyms-generate-imgt (from the root folder of this repository).

Contributing

Any contribution is welcome (especially adding/fixing documentation as that is very hard to do as main developer).