Crates.io | rustyms |
lib.rs | rustyms |
version | 0.8.3 |
source | src |
created_at | 2023-06-07 11:27:22.378986 |
updated_at | 2024-03-18 15:06:41.933454 |
description | A library to handle proteomic mass spectrometry data and match peptides to spectra. |
homepage | |
repository | https://github.com/snijderlab/rustyms |
max_upload_size | |
id | 884672 |
size | 17,022,424 |
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.
uom
for compile time unit checkingStitch
for more information, but the algorithm has been improved)# 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(()) }
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.