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Proteomes
Volume 8
Issue 3
10.3390/proteomes8030014
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Open AccessReview

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

by
Emmalyn J. Dupree
1,†,
Madhuri Jayathirtha
1,†,
Hannah Yorkey
1,
Marius Mihasan
2,*,
Brindusa Alina Petre
3,4,* and
Costel C. Darie
1,*
1
Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810, USA
2
Laboratory of Biochemistry & Molecular Biology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, 700506 Iasi, Romania
3
Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, 700506 Iasi, Romania
4
Center for Fundamental Research and Experimental Development in Translation Medicine–TRANSCEND, Regional Institute of Oncology, 700506 Iasi, Romania
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Proteomes 2020, 8(3), 14; https://doi.org/10.3390/proteomes8030014
Received: 1 June 2020 / Revised: 25 June 2020 / Accepted: 1 July 2020 / Published: 6 July 2020
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
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Abstract

Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future. View Full-Text
Keywords: mass spectrometry; proteomics; protein identification; protein characterization mass spectrometry; proteomics; protein identification; protein characterization
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
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MDPI and ACS Style

Dupree, E.J.; Jayathirtha, M.; Yorkey, H.; Mihasan, M.; Petre, B.A.; Darie, C.C. A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field. Proteomes 2020, 8, 14. https://doi.org/10.3390/proteomes8030014

AMA Style

Dupree EJ, Jayathirtha M, Yorkey H, Mihasan M, Petre BA, Darie CC. A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field. Proteomes. 2020; 8(3):14. https://doi.org/10.3390/proteomes8030014

Chicago/Turabian Style

Dupree, Emmalyn J.; Jayathirtha, Madhuri; Yorkey, Hannah; Mihasan, Marius; Petre, Brindusa A.; Darie, Costel C. 2020. "A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field" Proteomes 8, no. 3: 14. https://doi.org/10.3390/proteomes8030014

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