The Art of Validating Quantitative Proteomics Data

David C Handler; Dana Pascovici; Mehdi Mirzaei; Vivek Gupta; Ghasem Hosseini Salekdeh; Paul A Haynes

doi:10.1002/pmic.201800222

The Art of Validating Quantitative Proteomics Data

Proteomics. 2018 Dec;18(23):e1800222. doi: 10.1002/pmic.201800222. Epub 2018 Nov 25.

Authors

David C Handler¹, Dana Pascovici^{1

2}, Mehdi Mirzaei^{1

2}, Vivek Gupta³, Ghasem Hosseini Salekdeh^{1

4}, Paul A Haynes¹

Affiliations

¹ Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
² Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
³ Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
⁴ Department of Molecular Systems Biology, Cell Science Research Center Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.

PMID: 30352137
DOI: 10.1002/pmic.201800222

Abstract

Western blotting as an orthogonal validation tool for quantitative proteomics data has rapidly become a de facto requirement for publication. In this viewpoint article, the pros and cons of western blotting as a validation approach are discussed, using examples from our own published work, and how to best apply it to improve the quality of data published is outlined. Further, suggestions and guidelines for some other experimental approaches are provided, which can be used for validation of quantitative proteomics data in addition to, or in place of, western blotting.

Keywords: data quality; data validation; false discovery rate; shotgun proteomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Blotting, Western
Data Accuracy
Proteomics / methods*