MassJ.jl

<p align="center"> <h1 align="center"> MassJ.jl </h1> </p> <p align="center"> <img align="center" src="docs/src/assets/logo.png" width="400" height="200" /> </p> <p align="center"> <normal> A mass spectrometry package for Julia </normal> </p>

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:

pkg> add https://github.com/ajgiuliani/MassJ.jl

or using the package API:

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

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

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