Quantitative proteomics: challenges and opportunities in basic and applied research

Abstract

In this Perspective, we discuss developments in mass-spectrometry-based proteomic technology over the past decade from the viewpoint of our laboratory. We also reflect on existing challenges and limitations, and explore the current and future roles of quantitative proteomics in molecular systems biology, clinical research and personalized medicine.

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Figure 1: Standard mass spectrometry (MS)-based proteomics workflow and acquisition schemes.
Figure 2: A selection of methods used to explore the modular and spatial organization of the proteome.
Figure 3: Quantitative proteomics in molecular medicine.

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Acknowledgements

This work was supported by the Human Frontier Science Program (grant LT000737/2016 to O.T.S.), the Swiss National Science Foundation (R.A.; grant P2EZP3_165280 to O.T.S.; grant P2EZP3_162268 to H.L.R.; Ambizione grant PZ00P3_161435 to B.C.C.), EMBO (grant ALTF_854-2015 to H.L.R.), the Swiss Initiative for Systems Biology (SystemsX.ch; to R.A.) and the European Union via ERC (grant AdG-670821 to R.A.).

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O.T.S., H.L.R., B.C.C., G.R. and R.A. prepared the manuscript.

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Correspondence to Ruedi Aebersold.

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R.A. holds shares of Biognosys AG, which operates in the field covered by this Perspective.

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Schubert, O., Röst, H., Collins, B. et al. Quantitative proteomics: challenges and opportunities in basic and applied research. Nat Protoc 12, 1289–1294 (2017). https://doi.org/10.1038/nprot.2017.040

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