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MSj.jl

A mass spectrometry package for Julia

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Installation

This package is unregistered. It can be installed either with the Julia package manager. From the Julia REPL, type ] to enter the Pkg REPL mode and run:

(v1.3) pkg> add https://github.com/ajgiuliani/MSj.jl

or using the package API:

using Pkg
Pkg.add(PackageSpec(url="https://github.com/ajgiuliani/MSj.jl"))

Documentation

Documentation is available here.

Usage

MSj is a package for loading, processing and plotting mass spectrometry data. It provides the following functionalities:

Getting information on the file
Load a file
Averaging mass spectra based on various criteria that may be combined
Chromatogram and extracted chromatograms
Processing the data
    smoothing
    baseline correction
    peak-picking
Calculation of isotopic distribution

To get information on a file:

info("path/to/file")

Mass spectra can be loaded by:

data = load("path/to/file")

And averaged as follow:

ms1 = average(data, MSj.Level(1))                   # full MS scans
ms2 = average(data, MSj.Level(2))                   # MS2 spectra
ms3 = average(data, MSj.Activation_Method("CID"))   # CID spectra

See the documentation for additional information.

Supported file format

  • mzxml

Other Julia packages

  • mzXML.jl: Load mass spectrometry mzXML files.
  • MassSpec.jl: Mass spectometry utilities for Julia