R¹  is an open source environment and programming language for statistical computing. These features make it particularly well suited to address data intensive problems such as high-throughput biology. The Bioconductor project^2,3  is focused on the analysis and comprehension of high-throughput omics data; it provides over 1100 R packages and an active user and developer community of wet-lab biologists, computer scientists, computational biologists and statisticians. Mass spectrometry and proteomics are heavily dependent on the exploitation of advanced computing, visualisation and statistical technologies, and the Bioconductor project has, in recent years, benefited from numerous contributions from the mass spectrometry and...