MassJ.jl

A mass spectrometry package for Julia

Installation

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

pkg> add MassJ

or using the package API:

using Pkg
Pkg.add("MassJ")

Documentation

Documentation is available here.

Usage

MassJ 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
Charge states deconvolution

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

See the documentation for additional information.

Supported file format

• mzxml
• mzML
• MGF
• MSP
• imzML
• txt

Other Julia packages

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