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Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric

Proteomes Are of Proteoforms: Embracing the Complexity

Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
Author to whom correspondence should be addressed.
Academic Editor: Julian Whitelegge
Proteomes 2021, 9(3), 38;
Received: 1 August 2021 / Revised: 24 August 2021 / Accepted: 29 August 2021 / Published: 31 August 2021
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
Proteomes are complex—much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current ‘state-of-the-field’. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy? View Full-Text
Keywords: proteomics; top-down; bottom-up; immunoassay; mass spectrometry; two-dimensional gel electrophoresis; Western blotting proteomics; top-down; bottom-up; immunoassay; mass spectrometry; two-dimensional gel electrophoresis; Western blotting
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MDPI and ACS Style

Carbonara, K.; Andonovski, M.; Coorssen, J.R. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021, 9, 38.

AMA Style

Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes. 2021; 9(3):38.

Chicago/Turabian Style

Carbonara, Katrina, Martin Andonovski, and Jens R. Coorssen. 2021. "Proteomes Are of Proteoforms: Embracing the Complexity" Proteomes 9, no. 3: 38.

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