Module mzdata::spectrum

The data structures and components that represent a mass spectrum and how to access their data.

A mass spectrum is made up of multiple components, the spectrum’s signal data itself, plus all the metadata that describes how that data was acquired by the instrument.

Components

• bindata includes structures for dealing with raw binary data arrays that may or may not be byte-encoded but not strongly typed, though it does not include signal processing as that is outside the scope of this crate.

Spectra

Represent the collection of attributes and data that compose a single mass spectrum.

Because a mass spectrum may be obtained from sources with varying levels of detail, several alternative structures are provided with a common set of trait-based methods to unify access:

1. RawSpectrum for representing a spectrum that has not been decoded into distinct peaks yet, but whose data may be continuous or discrete.
2. CentroidSpectrum for representing spectra from sources which are guaranteed to be pre-centroided, like those from MGF files or other simple text representations.
3. Spectrum for representing a multi-layer representation of a spectrum where both raw data and a distinct peak list are available.

These structures all implement the SpectrumDescription trait

The SpectrumDescription trait is included in the crate prelude, and gives the caller read-only access to components that describe a spectrum’s metadata.

use mzpeaks::Tolerance;
use mzdata::MzMLReader;
use mzdata::prelude::*;
use mzdata::spectrum::SignalContinuity;

let reader = MzMLReader::open_path("./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)));
    }
}

Re-exports

• pub use crate::spectrum::bindata::ArrayType;
• pub use crate::spectrum::bindata::BinaryArrayMap;
• pub use crate::spectrum::bindata::BinaryDataArrayType;
• pub use crate::spectrum::bindata::DataArray;

Modules

• bindata
• utils

Structs

• Acquisition
  Describe the series of acquisition events that constructed the spectrum being described.
• Activation
  Describes the activation method used to dissociate the precursor ion
• CentroidSpectrumType
  Represents a spectrum that has been centroided
• Chromatogram
• ChromatogramDescription
  The set of descriptive metadata that give context for how a chromatogram was recorded.
• DeconvolutedSpectrumType
  Represents a spectrum that has been centroided, deisotoped, and charge state deconvolved
• DeferredSpectrumAveragingIterator
• IsolationWindow
  The interval around the precursor ion that was isolated in the precursor scan. Although an isolation window may be specified either with explicit bounds or offsets from the target, this data structure always uses explicit bounds once it is in a IsolationWindowState::Complete .
• MultiLayerSpectrum
  Represent a spectrum with multiple layers of representation of the peak data.
• Precursor
  Describes the precursor ion of the owning spectrum.
• RawSpectrum
  Represents a spectrum that hasn’t been processed yet, with only data arrays, potentially no discrete peaks.
• ScanEvent
  Describes a single scan event. Unless additional post-processing is done, there is usually only one event per spectrum.
• ScanWindow
  The m/z range which was scanned
• SelectedIon
  Describes a single selected ion from a precursor isolation
• SpectrumAveragingIterator
  Wrap a [SpectrumGroupingIterator] to average MS1 spectra over
• SpectrumDescription
  The set of descriptive metadata that give context for how a mass spectrum was acquired within a particular run. This forms the basis for a large portion of the SpectrumDescription trait.
• SpectrumGroup
  A pairing of an optional MS1 spectrum with all its associated MSn spectra.
• SpectrumGroupIntoIter
• SpectrumGroupIter
  Iterate over the spectra in SpectrumGroup
• SpectrumGroupingIterator
  A wrapper for Iterator-implementors that will batch together all MSn spectra with their associated MS1 spectrum, producing SpectrumGroup instances.

Enums

• ActivationMethod
• ChromatogramType
  Types of chromatograms enumerated in the PSI-MS controlled vocabulary
• IsolationWindowState
  Describe the initialization stage of an isolation window
• PeakDataLevel
• RefPeakDataLevel
  An variant for dispatching to different strategies of computing common statistics of different levels of peak data.
• ScanCombination
  Represents means by which a spectrum is generated using one or more instrument analyzers
• ScanPolarity
  Describes the polarity of a mass spectrum. A spectrum is either Positive (1+), Negative (-1) or Unknown (0). The Unknown state is the default.
• SignalContinuity
  Describes the initial representation of the signal of a spectrum.
• SpectrumConversionError
  Errors that may arise when converting between different SpectrumBehavior-like types
• SpectrumProcessingError
  Errors that may arise when performing signal processing or other data transformation

Traits

• CentroidPeakAdapting
  A blanket trait that ties together all the assumed behaviors of an m/z coordinate centroid peak
• ChromatogramLike
• DeconvolutedPeakAdapting
  A blanket trait that ties together all the assumed behaviors of an neutral mass coordinate centroid peak
• IonMobilityMeasure
• IonProperties
  Describe the precursor ion that this entity represents
• PrecursorSelection
  A trait for abstracting over how a precursor ion is described, immutably.
• SpectrumGroupAveraging
  Adds signal averaging to an Iterator that produces SpectrumGrouping implementations of the appropriate type.
• SpectrumLike
  A trait for providing a uniform delegated access to spectrum metadata

Functions

• average_spectra
  Average a series of MultiLayerSpectrum together

Type Aliases

• CentroidSpectrum
• DeconvolutedSpectrum
• Spectrum
  A ready-to-use parameterized type for representing a spectrum in multiple overlapping layers.