The incongruity of validating quantitative proteomics using western blots

Abstract

Similar to the age-old reviewer request for quantitative PCR validation of RNA sequencing data, nearly every researcher using proteomics technologies has, at one time or another, been asked by a reviewer to provide “western blot validation” of their mass spectrometry-based protein abundance data. We believe this request demonstrates a lack of awareness amongst the plant biology community about the extraordinary improvements in cost, sensitivity and reliability the field of mass spectrometry-based proteomics has made in recent years. Here, in this study, as a group of experts in different domains of quantitative plant proteomics, we explain why “western blot validation” of quantitative proteomics data is both unnecessary and invalid. Furthermore, we invite our colleagues in the plant science community to update their perception of quantitative mass spectrometry as a sensitive and reliable method of protein identification and quantitation.