Match those fragments!

Handle mass spectrometry data in Rust. This crate is set up to handle very complex peptides with loads of ambiguity and complexity. It pivots around the [ComplexPeptide] and [LinearPeptide] which encode the ProForma specification. Additionally this crate enables the reading of mgf, doing spectrum annotation (BU/MD/TD), finding isobaric sequences, doing alignments of peptides , accessing the IMGT germline database, and reading identified peptide files.

Library 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)

Example usage

# fn main() -> Result<(), rustyms::error::CustomError> {
# let raw_file_path = "data/annotated_example.mgf";
// Open some data and see if the given peptide is a valid match
use rustyms::{*, system::{Charge, e}};
let peptide = ComplexPeptide::pro_forma("Q[Gln->pyro-Glu]VQEVSERTHGGNFD")?;
let spectrum = rawfile::mgf::open(raw_file_path)?;
let model = Model::ethcd();
let fragments = peptide.generate_theoretical_fragments(Charge::new::<e>(2.0), &model);
let annotated = spectrum[0].annotate(peptide, &fragments, &model, MassMode::Monoisotopic);
let fdr = annotated.fdr(&fragments, &model);
// This is the incorrect sequence for this spectrum so the FDR will indicate this
# dbg!(&fdr, fdr.sigma(), fdr.fdr(), fdr.score());
assert!(fdr.sigma() < 2.0);
# Ok(()) }

# fn main() -> Result<(), rustyms::error::CustomError> {
// Check how this peptide compares to a similar peptide (using `align`)
// (same sequence, repeated for easy reference)
use rustyms::{*, align::*};
let first_peptide = LinearPeptide::pro_forma("Q[Gln->pyro-Glu]VQEVS")?;
let second_peptide = LinearPeptide::pro_forma("E[Glu->pyro-Glu]VQVES")?;
let alignment = align::<4>(&first_peptide, &second_peptide,
                 matrix::BLOSUM62, Tolerance::new_ppm(10.0), AlignType::GLOBAL);
# dbg!(&alignment);
let stats = alignment.stats();
# //assert_eq!(stats.identical, 3); // Only three positions are identical
assert_eq!(stats.mass_similar, 6); // All positions are mass similar
# Ok(()) }

Compilation features

Rustyms ties together multiple smaller modules into one cohesive structure. It has multiple features which allow you to slim it down if needed (all are enabled by default).

• identification - gives access to methods reading many different identified peptide formats.
• align - gives access to mass based alignment of peptides.
• imgt - enables access to the IMGT database of antibodies germline sequences, with annotations.
• rayon - enables parallel iterators using rayon, mostly for imgt but also in consecutive align.