Mass spectrometry analysis using MALDIquant

TL;DR

MALDIquant offers a comprehensive open-source R platform for analyzing 2D mass spectrometry data, demonstrated through a cancer dataset analysis from raw data to classification.

Contribution

This paper introduces MALDIquant, an open-source R package with methods and algorithms for mass spectrometry data analysis, including a complete workflow example.

Findings

Effective analysis of cancer mass spectrometry data

Successful classification of samples using MALDIquant

Demonstrates versatility of the open-source platform

Abstract

MALDIquant and associated R packages provide a versatile and completely free open-source platform for analyzing 2D mass spectrometry data as generated for instance by MALDI and SELDI instruments. We first describe the various methods and algorithms available in MALDIquant . Subsequently, we illustrate a typical analysis workflow using MALDIquant by investigating an experimental cancer data set, starting from raw mass spectrometry measurements and ending at multivariate classification.