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Review
. 2020 Jul 6;8(3):14.
doi: 10.3390/proteomes8030014.

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

Emmalyn J Dupree  1 , Madhuri Jayathirtha  1 , Hannah Yorkey  1 , Marius Mihasan  2 , Brindusa Alina Petre  3   4 , Costel C Darie  1
Affiliations
Review

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

Emmalyn J Dupree et al. Proteomes. .

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.

Keywords: mass spectrometry; protein characterization; protein identification; proteomics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Workflow in a bottom-up proteomics experiment.
Figure 2
Figure 2
Correspondence between the peptide’s amino acid sequence and the fragment ion peaks that are produced in MS/MS (A) and the major theoretical fragment ions that are produced from fragmentation of a peptide (B).
See this image and copyright information in PMC

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