Crate mzsignal

mzsignal is a library for performing low-level signal processing on mass spectra en-route to converting a continuous profile-mode spectrum into a centroided peak list.

The peak picking facility can be used directly with PeakPicker which implements a simple gaussian peak shape fitter. There are a some threshold criteria that can be manipulated to control which fits are reported, see its documentation for more details.

When one spectrum is too noisy to accurately assign peaks, averaging the signal from multiple spectra together can be better. The average submodule includes components for merging together multiple profile spectra.

The denoise submodule includes an algorithm for local background noise removal, reducing the intensity of a region according to its noisiest window.

The reprofile submodule provides an algorithm to convert a centroid peak back into a profile spectrum, using either fitted or assumed peak shape parameters.

Usage

use std::fs;
use std::io;
use std::io::prelude::*;

use mzsignal;

let mut mz_array: Vec<f64> = Vec::new();
let mut intensity_array: Vec<f32> = Vec::new();

// Read in signal arrays from a text file
let reader = io::BufReader::new(fs::File::open("./test/data/test.txt").unwrap());
for line in reader.lines() {
    let line = line.unwrap();
    let pref = line.trim();
    let chunks: Vec<&str> = pref.split("\t").collect();
    mz_array.push(chunks[0].parse::<f64>().expect("Expected number for m/z"));
    intensity_array.push(chunks[1].parse::<f32>().expect("Expected number for intensity"));
}

// Create a peak picker
let picker = mzsignal::PeakPicker::default();

// Create an accumulator
let mut acc = Vec::new();

// Pick peaks
let peak_count = picker.discover_peaks(&mz_array, &intensity_array, &mut acc).unwrap();
assert_eq!(peak_count , 4);
for peak in acc.iter() {
    println!("{}", peak);
}

Data Ownership

Most algorithms in mzsignal require ownly a borrowed view of the m/z dimension of a spectrum, creating a new array of different size if appropriate. The intensity array is almost always re-allocated to fit the new m/z array shape.

When possible, the data structures in average, SignalAverager, and reprofile, PeakSetReprofiler will own their high density m/z arrays and can be re-used from spectrum to spectrum to avoid repeatedly allocating that large array, and leave it to be borrowed again later. The high level functions in these modules create new data structures to exactly fit the m/z ranges they are given on every call, slowing them down by comparison if used over and over again. In both cases, even if the reference m/z range is much larger than the region needed for a particular input’s, only the required region will be used for any given computation.

Building

This library needs a small amount of linear algebra, so it depends on either nalgebra or ndarray+ndarray-linalg.

If the you wish to use ndarray-linalg, it needs a LAPACK implementation, controlled by the following features:

• intel-mkl
• openblas
• netlib

otherwise, the default nalgebra backend will be used.

Re-exports

• pub use crate::arrayops::ArrayPair;
• pub use crate::peak::FittedPeak;
• pub use crate::peak_picker::pick_peaks;
• pub use crate::peak_picker::PeakFitType;
• pub use crate::peak_picker::PeakPicker;
• pub use crate::peak_picker::PeakPickerError;

Modules

• arrayops
  Helper functions and data structures for manipulating array data
• average
  Re-bin a single spectrum, or average together multiple spectra using interpolation.
• denoise
  Remove local noise from a spectrum using the denoising algorithm from MasSpike.
• histogram
• peak
• peak_picker
• peak_statistics
• reprofile
  Convert picked peaks into a profile spectrum.
• search
  A set of low level coordinate search code. Not necessary for external use.
• smooth
  An implementation of smoothing filters and transformations
• text
  Helpers for loading test data