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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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References

    1. Schwenk J.M., Omenn G.S., Sun Z., Campbell D.S., Baker M.S., Overall C.M., Aebersold R., Moritz R.L., Deutsch E.W. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. J. Proteome Res. 2017;16:4299–4310. doi: 10.1021/acs.jproteome.7b00467. - DOI - PMC - PubMed
    1. Chen D., Li X.Y., Zhao X., Qin Y.S., Zhang X.X., Li J., Wang J.M., Wang C.F. Proteomics and microstructure profiling of goat milk protein after homogenization. J. Dairy Sci. 2019;102:3839–3850. doi: 10.3168/jds.2018-15363. - DOI - PubMed
    1. Mohanta T.K., Khan A., Hashem A., Abd Allah E.F., Al-Harrasi A. The molecular mass and isoelectric point of plant proteomes. BMC Genom. 2019;20:631. doi: 10.1186/s12864-019-5983-8. - DOI - PMC - PubMed
    1. Aslam B., Basit M., Nisar M.A., Khurshid M., Rasool M.H. Proteomics: Technologies and Their Applications. J. Chromatogr. Sci. 2017;55:182–196. doi: 10.1093/chromsci/bmw167. - DOI - PubMed
    1. Swinbanks D. Australia Backs Innovation, Shuns Telescope. Nature. 1995;378:653. doi: 10.1038/378653a0. - DOI - PubMed