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Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):449-72. doi: 10.1146/annurev-anchem-071015-041535. Epub 2016 Mar 30.

Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing.

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Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; email:
Faculty of Science, University of Zürich, 8057 Zürich, Switzerland.


Proteins constitute a key class of molecular components that perform essential biochemical reactions in living cells. Whether the aim is to extensively characterize a given protein or to perform high-throughput qualitative and quantitative analysis of the proteome content of a sample, liquid chromatography coupled to tandem mass spectrometry has become the technology of choice. In this review, we summarize the current state of mass spectrometry applied to bottom-up proteomics, the approach that focuses on analyzing peptides obtained from proteolytic digestion of proteins. With the recent advances in instrumentation and methodology, we show that the field is moving away from providing qualitative identification of long lists of proteins to delivering highly consistent and accurate quantification values for large numbers of proteins across large numbers of samples. We believe that this shift will have a profound impact for the field of proteomics and life science research in general.


data-dependent acquisition; data-independent acquisition; peptide-centric; shotgun proteomics; spectrum-centric; targeted proteomics

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