Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view

BACKGROUND: For decades, mass spectrometry data has been analyzed to investigate a wide array of research interests, including disease diagnostics, biological and chemical theory, genomics, and drug development. Progress towards solving any of these disparate problems depends upon overcoming the common challenge of interpreting the large data sets generated. Despite interim successes, many data interpretation problems in mass spectrometry are still challenging. Further, though these challenges are inherently interdisciplinary in nature, the significant domain-specific knowledge gap between disciplines makes interdisciplinary contributions difficult. RESULTS: This paper provides an introduction to the burgeoning field of computational mass spectrometry. We illustrate key concepts, vocabulary, and open problems in MS-omics, as well as provide invaluable resources such as open data sets and key search terms and references. CONCLUSIONS: This paper will facilitate contributions from mathematicians, computer scientists, and statisticians to MS-omics that will fundamentally improve results over existing approaches and inform novel algorithmic solutions to open problems.