I haven't done any mass spectrometry since the Johnson Administration, so I can only suggest doing a search for that term on rseek.org and these packages from the taskview
Mass Spectrometry
The MSnbase defines infrastructure for mass spectrometry-based proteomics data handling, plotting, processing and quantification.
The MALDIquant provides tools for quantitative analysis of MALDI-TOF mass spectrometry data, with support for baseline correction, peak detection and plotting of mass spectra.
The OrgMassSpecR package is for organic/biological mass spectrometry, with a focus on graphical display, quantification using stable isotope dilution, and protein hydrogen/deuterium exchange experiments.
The FTICRMS package provides functions for Analyzing Fourier Transform-Ion Cyclotron ed Resonance Mass Spectrometry Data.
The titan provides a GUI to analyze mass spectrometric data on the relative abundance of two substances from a titration series.
The Bioconductor packages MassSpecWavelet, PROcess, and xcms are designed for the analysis of mass spectrometry data.
The apLCMS package is designed for the processing of LC/MS based metabolomics data.
The xMSanalyzer package allows merging apLCMS sample processing results from multiple sets of parameter settings, among other features.
The MSPrep package is for post-processing of metabolomic data, including summarization of replicates, filtering, imputation, and normalization.
The metaMS package is an MS-based metabolomics data processing and compound annotation pipeline.