Crate mzdata

mzdata provides basic access to raw and processed mass spectrometry data formats in Rust.

The library currently supports reading:

1. MGF files using MGFReader in mzdata::io::mgf
2. mzML & indexedmzML files using MzMLReader in mzdata::io::mzml
3. mzMLb files using MzMLbReader in mzdata::io::mzmlb

and writing:

1. MGF files using MGFWriter in mzdata::io::mgf
2. mzML & indexedmzML files using MzMLWriter in mzdata::io::mzml
3. mzMLb files using MzMLbWriter in mzdata::io::mzmlb

It also includes a set of representation layers for spectra in mzdata::spectrum

Example

use std::fs;
use mzdata::prelude::*;
use mzpeaks::{Tolerance, prelude::*};
use mzdata::io::MzMLReader;
use mzdata::spectrum::{SignalContinuity};
let reader = MzMLReader::new(fs::File::open("./test/data/small.mzML").unwrap());
for spectrum in reader {
    println!("Scan {} => BP {}", spectrum.id(), spectrum.peaks().base_peak().mz);

    if spectrum.signal_continuity() < SignalContinuity::Profile {
        let peak_picked = spectrum.into_centroid().unwrap();
        println!("Matches for 579.155: {:?}",
                 peak_picked.peaks.all_peaks_for(
                    579.155, Tolerance::Da(0.02)
                )
        );
    }
}

It uses mzpeaks to represent peaks and peak lists, and re-exports the basic types. While the high-level types are templated on simple peak types, more complex, application-specific peak types can be substituted. See mzdata::spectrum::bindata for more information about how to directly convert data arrays to peak lists.

Traits

The library makes heavy use of traits to abstract over the implementation details of different file formats. These traits are included in mzdata::prelude.

Re-exports

• pub use crate::io::mgf::MGFError;
• pub use crate::io::mgf::MGFReader;
• pub use crate::io::mgf::MGFWriter;
• pub use crate::io::mzml::MzMLParserError as MzMLError;
• pub use crate::io::mzml::MzMLReader;
• pub use crate::io::mzml::MzMLWriter;
• pub use crate::io::mzml::MzMLWriterError;
• pub use crate::io::mzmlb::MzMLbError;
• pub use crate::io::mzmlb::MzMLbReader;
• pub use crate::io::mzmlb::MzMLbWriter;
• pub use crate::io::mzmlb::MzMLbWriterBuilder;
• pub use crate::io::mzmlb::MzMLbWriterError;
• pub use crate::params::Param;
• pub use crate::params::ParamList;
• pub use crate::spectrum::CentroidSpectrum;
• pub use crate::spectrum::RawSpectrum;
• pub use crate::spectrum::Spectrum;

Modules

• io
  Reading and writing mass spectrometry data file formats and abstractions over them.
• meta
  Metadata describing mass spectrometry data files and their contents.
• params
  Elements of controlled vocabularies used to describe mass spectra and their components.
• prelude
  A set of foundational traits used throughout the library.
• spectrum
  The data structures and components that represent a mass spectrum and how to access their data.

Macros

• delegate_impl_metadata_trait
  Delegates the implementation of MSDataFileMetadata to an field
• impl_metadata_trait
  Assumes a field for the non-Option facets of the MSDataFileMetadata implementation are present.
• impl_param_described
• impl_param_described_deferred