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Mass spectrometry is the workhorse technology to study the abundance and composition of proteins, the key players in every living cell. Within the last decade the technology experienced a revolution in terms of novel instrumentation and optimized sample handling protocols resulting in ever growing numbers of proteins and post-translational modifications that can be routinely studied on a system-wide scale. Briefly, proteins are extracted from cells or tissues and fragmented into smaller peptides. This extremely complex peptide mixture is subjected to liquid chromatography separation and subsequent tandem mass spectrometry analysis in which mass-to-charge ratios of intact peptides and peptide fragments are recorded. Resulting mass spectra are matched to sequence databases or spectral libraries to read out the amino acid sequences and thereby identify the corresponding proteins.

The technology is fundamentally different from sequencing-based genomics technology and faces different problems, such as the tremendous dynamic range of protein expression. The instruments can be operated in different acquisition modes for different applications. I will briefly introduce the basics behind discovery or ‘shotgun’ proteomics, targeted proteomics, data dependent acquisition and data independent acquisition; the latter is a recent and promising development in the proteomics community but poses novel and only partly solved challenges in data analysis. Ryan Peckner will talk about Specter, an approach that tackles this problem using linear algebra.