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In this chapter, we introduce some R and Bioconductor software to process, analyse and interpret mass spectrometry and proteomics data. We describe how to programmatically access data, how to read various data formats into R, we review the existing infrastructure to reliably identify peptide-spectrum matches, describe how to analyse and process quantitative data, review MALDI and imaging mass spectrometry using Bioconductor packages and conclude with an overview of statistical and machine learning software applicable to proteomics data. All the use cases are accompanied by executable example code and further reproducible examples are provided in the companion RforProteomics package.

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