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Proteomics: a pragmatic perspective

Abstract

The evolution of mass spectrometry–based proteomic technologies has advanced our understanding of the complex and dynamic nature of proteomes while concurrently revealing that no 'one-size-fits-all' proteomic strategy can be used to address all biological questions. Whereas some techniques, such as those for analyzing protein complexes, have matured and are broadly applied with great success, others, such as global quantitative protein expression profiling for biomarker discovery, are still confined to a few expert laboratories. In this Perspective, we attempt to distill the wide array of conceivable proteomic approaches into a compact canon of techniques suited to asking and answering specific types of biological questions. By discussing the relationship between the complexity of a biological sample and the difficulty of implementing the appropriate analysis approach, we contrast areas of proteomics broadly usable today with those that require significant technical and conceptual development. We hope to provide nonexperts with a guide for calibrating expectations of what can realistically be learned from a proteomics experiment and for gauging the planning and execution effort. We further provide a detailed supplement explaining the most common techniques in proteomics.

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Figure 1: Conceptual organization of proteomic experiments.
Figure 2: Applications of proteomic technologies.
Figure 3: Technologies for proteomics.
Figure 4: Protein identification and quantification by mass spectrometry.

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Acknowledgements

The authors thank M. Bergman, C. Flinders, K. Kramer and S. Mumenthaler for comments on the manuscript. The work of P.M. was supported by NCI-1U54CA143907 and NCI-U54CA119367.

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Mallick, P., Kuster, B. Proteomics: a pragmatic perspective. Nat Biotechnol 28, 695–709 (2010). https://doi.org/10.1038/nbt.1658

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