Crate rustyms

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)

Re-exports

• pub use crate::model::Model;
• pub use crate::modification::Modification;
• pub use crate::spectrum::AnnotatedSpectrum;
• pub use crate::spectrum::MassMode;
• pub use crate::spectrum::RawSpectrum;
• pub use fragment::Fragment;

Modules

• align
  A module to contain all alignment related structures and algorithms.
• error
  Contain the definition for errors with all additional data that is needed to generate nice error messages
• fragment
  Handle fragment related issues, access provided if you want to dive deeply into fragments in your own code.
• glycan
  Handle glycan related issues, access provided if you want to work with glycans on your own.
• identifications
  Read in the annotations from peptide identification sources
• model
  Handle model instantiation.
• modification
  Handle modification related issues, access provided if you want to dive deeply into modifications in your own code.
• rawfile
  Handling raw files
• spectrum
  Spectrum related code
• system
  The measurement system used in this crate. A redefinition of the important SI units for them to be stored in a more sensible base unit for MS purposes.

Macros

• Q
  Macro to implement quantity type aliases for a specific system of units and value storage type.
• formula_internal
  Internal code for the molecular_formula macro.
• molecular_formula
  Easily define molecular formulas using the following syntax: <element> <num> or (<isotope>)<element> <num>

Structs

• LinearPeptide
  A peptide with all data as provided by pro forma. Preferably generated by using the crate::ComplexPeptide::pro_forma function.
• MolecularFormula
  A molecular formula, a selection of elements of specified isotopes together forming a structure
• SequenceElement
  One block in a sequence meaning an aminoacid and its accompanying modifications

Enums

• AminoAcid
  An amino acid, alongside the standard ones some ambiguous (J/X) and non-standard (U/O) are included. https://www.insdc.org/submitting-standards/feature-table/#7.4.3
• ComplexPeptide
  A single pro forma entry, can contain multiple peptides
• Element
  The elements (and electrons)
• MassTolerance
  A tolerance around a given mass for searching purposes
• NeutralLoss
  All possible neutral losses

Constants

• ELEMENT_PARSE_LIST
  All elements sorted so that single characters come after two character element symbols (needed for greedy parsing)

Traits

• Chemical
  Any item that has a clearly defined molecular formula

Functions

• elemental_data
  Get the elemental data
• find_isobaric_sets
  Find the isobaric sets for the given mass with the given modifications and ppm error. The modifications are placed on any location they are allowed based on the given placement rules, so using any modifications which provide those is advised.