MSnbase, Comprehensive Skill Guide

Domain: Proteomics / Mass spectrometry Bioconductor: MSnbase Paper: Gatto L, Lilley KS (2012). Bioinformatics, 28(2):288-289.

Infrastructure for mass spectrometry data handling in R: reading mzML/mzXML/mzData files, spectral processing, quantification, and proteomics/metabolomics workflows.

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 2.37.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: BiocGenerics, Biobase, mzR, S4Vectors, ProtGenerics
• Imports: MsCoreUtils, PSMatch, BiocParallel, IRanges, plyr, vsn, affy, impute, pcaMethods, MALDIquant, mzID, digest, lattice, ggplot2, scales, MASS, Rcpp
• Install: BiocManager::install("MSnbase")

When to Use

• Read mzML/mzXML files into R for proteomics or metabolomics workflows
• Process MS2 spectra: deisotoping, centroiding, filtering
• TMT/iTRAQ isobaric quantification
• Feature quantification from LC-MS data

Alternatives: Spectra (modern successor), openms (Python/C++), msqrob2 (DE protein)

Do NOT Use When

• Large-scale DIA proteomics, use PyProphet/OpenSWATH or Spectronaut.
• Metabolomics spectral matching, use Spectra + CompoundDb instead.
• New projects, consider Spectra as the modern successor.

Data Requirements

Requirement	Details
Input Format	mzML, mzXML, mzData (open MS formats; convert with ProteoWizard)
Notes	Use mode='onDisk' for files > 1GB to avoid memory issues

Installation

if (!require("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("MSnbase")
library(MSnbase)

Workflows

Read and Process LC-MS Data for Proteomics

Load mzML files, filter spectra, and perform isobaric quantification

Read mzML files (on-disk mode)