🦀 Rust: 🐍 Python:

Match those fragments!

A peptide fragmentation matching library for rust. Split into multiple smaller crates to help keep things organised.

Features

• Read pro forma sequences ('level 2-ProForma + mass spectrum compliant + glycans compliant', with the intention to fully support the whole spec)
• Generate theoretical fragments with control over the fragmentation model from any supported pro forma peptide
  • Generate fragments from satellite ions (w, d, and v)
  • Generate glycan fragments
  • Generate theoretical fragments for modifications of unknown position
  • Generate theoretical fragments for chimeric spectra
• Read mgf files
• Match spectra to the generated fragments
• Extensive use of uom for compile time unit checking
• Align peptides based on mass
• Fast access to the IMGT database of antibody germlines
• Reading of multiple identified peptide file formats (both de novo and database matching)

Python bindings

Python bindings are provided to several core components of the rustyms library. Go to the Python documentation for more information.

Contributing

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

IMGT generate

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