MALDIquant: a versatile R package for the analysis of mass spectrometry data

TL;DR

MALDIquant is a comprehensive R package designed for the analysis of mass spectrometry data, with features tailored for clinical diagnostics, including data import, preprocessing, peak alignment, and calibration.

Contribution

It introduces a modular, versatile R package that handles raw data import, preprocessing, and alignment for mass spectrometry, supporting clinical diagnostic applications.

Findings

Supports technical replicates and spectra with unequal resolution

Provides sophisticated routines for peak alignment and calibration

Available as open-source software with documentation and example data

Abstract

Summary: MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak alignment, and calibration. It also handles technical replicates as well as spectra with unequal resolution. Availability: MALDIquant and its associated R packages readBrukerFlexData and readMzXmlData are freely available from the R archive CRAN (http://cran.r-project.org). The software is distributed under the GNU General Public License (version 3 or later) and is accompanied by example files and data. Additional documentation is available from http://strimmerlab.org/software/maldiquant/.