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Review

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

Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205, USA
Academic Editors: Jens R. Coorssen and Matthew P. Padula
Proteomes 2021, 9(3), 34; https://doi.org/10.3390/proteomes9030034
Received: 2 July 2021 / Revised: 13 July 2021 / Accepted: 15 July 2021 / Published: 20 July 2021
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
Proteomic technology has improved at a staggering pace in recent years, with even practitioners challenged to keep up with new methods and hardware. The most common metric used for method performance is the number of peptides and proteins identified. While this metric may be helpful for proteomics researchers shopping for new hardware, this is often not the most biologically relevant metric. Biologists often utilize proteomics in the search for protein regulators that are of a lower relative copy number in the cell. In this review, I re-evaluate untargeted proteomics data using a simple graphical representation of the absolute copy number of proteins present in a single cancer cell as a metric. By comparing single-shot proteomics data to the coverage of the most in-depth proteomic analysis of that cell line acquired to date, we can obtain a rapid metric of method performance. Using a simple copy number metric allows visualization of how proteomics has developed in both sensitivity and overall dynamic range when using both relatively long and short acquisition times. To enable reanalysis beyond what is presented here, two available web applications have been developed for single- and multi-experiment comparisons with reference protein copy number data for multiple cell lines and organisms. View Full-Text
Keywords: proteomics; protein informatics; mass spectrometry; single cell; copy number proteomics; protein informatics; mass spectrometry; single cell; copy number
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MDPI and ACS Style

Orsburn, B.C. Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric. Proteomes 2021, 9, 34. https://doi.org/10.3390/proteomes9030034

AMA Style

Orsburn BC. Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric. Proteomes. 2021; 9(3):34. https://doi.org/10.3390/proteomes9030034

Chicago/Turabian Style

Orsburn, Benjamin C. 2021. "Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric" Proteomes 9, no. 3: 34. https://doi.org/10.3390/proteomes9030034

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