Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry

Published

June 4, 2024

Author(s)

Yuming Jiang, Devasahayam Rex, Dina Schuster, Ben Neely, German Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton Peters-Clarke, Susan Egbert, Simion Kreimer, Emma Doud, Oliver Cook, Amit Yadav, Muralidharan Vanuopadath, Martin Mayta, Anna Duboff, Nicholas Riley, Robert Moritz, Jesse Meyer

Abstract

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.

Citation

ACS Measurement Science Au

Pub Type

Journals

Download Paper

https://doi.org/10.1021/acsmeasuresciau.3c00068

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Keywords

proteomics, mass spectrometry, bottom-up proteomics

Citation

Jiang, Y. , Rex, D. , Schuster, D. , Neely, B. , Rosano, G. , Volkmar, N. , Momenzadeh, A. , Peters-Clarke, T. , Egbert, S. , Kreimer, S. , Doud, E. , Cook, O. , Yadav, A. , Vanuopadath, M. , Mayta, M. , Duboff, A. , Riley, N. , Moritz, R. and Meyer, J. (2024), Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry, ACS Measurement Science Au, [online], https://doi.org/10.1021/acsmeasuresciau.3c00068, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=957033 (Accessed March 14, 2025)