Match those fragments!

A peptide fragmentation matching library for rust.

use rustyms::*;
use rustyms::system::*;
// Parse a peptide
let peptide = ComplexPeptide::pro_forma("VAEINPSNGGTTFNEKFKGGKATJ").unwrap();
// Get the theoretical fragmentation for EThcD
let fragments = peptide.generate_theoretical_fragments(Charge::new::<e>(4.0), &Model::ethcd()).unwrap();
// Load the raw file
let spectra = rawfile::mgf::open("data/annotated_example.mgf").unwrap();
// Annotate the spectrum with this peptide
let matched = spectra[0].annotate(peptide, &fragments, &Model::ethcd(), MassMode::Monoisotopic);

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 (algorithm will be tweaked extensively over time) (see Stitch for more information, but the algorithm has been improved)