The Art of Validating Quantitative Proteomics Data

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


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*