Ambiguity of protein abbreviation PDK1: Error categorization and propagation analysis

Abstract

Despite peer review, hundreds of biomedical articles contain errors due to identical abbreviations that refer to different proteins. This includes PDK1, denoting both pyruvate dehydrogenase kinase 1 and 3-phosphoinositide-dependent protein kinase 1. Our analysis shows that one-out-of-five articles with the term PDK1 on PubMed, published in 2019-2026, state incorrect antibodies, refer to incorrect sequences for PCR, gene silencing, or plasmids, merge the properties of the two proteins, or incorrectly cite the other protein. Confusion extends to websites of biotechnology providers, where PDK1 antibodies and recombinant proteins were misattributed. To mitigate PDK1 abbreviation misuse, we recommend using unique protein abbreviations, clear antibody and sequence identification, and implementation of more rigorous peer review processes, supported by our newly developed PDK1-TermTracker citation network visualization and analysis service.