Detection of Viral Proteins in Human Cells Lines by Xeno-Proteomics: Elimination of the Last Valid Excuse for Not Testing Every Cellular Proteome Dataset for Viral Proteins

Chernobrovkin, Alexey L.; Zubarev, Roman A.

This alarming example suggests that the problem of cell line contamination is widespread and it cannot be dismissed as a malpractice within a few poorly managed laboratories. The vast majority of current microbial or viral infection tests are based on PCR, ELISA and other methods targeting specific organisms. In contrast, untargeted omics techniques (genomics, transcriptomics and proteomics) provide complete or very significant coverage of the respective domain, practically eliminating the risk of missing a contaminant in the dataset provided the genome of the contaminant is known. However, the data analysis methods used today in e.g. shotgun proteomics of cell lines, are often blind to other organisms than the target one. The standard protocol simply discards the data that do not fit into genome of the host organism, thus ignoring, and in some cases misattributing, even significant contamination [17, 18] . In view of the above scary examples of misattribution, such a practice should be discouraged, and a better procedure needs to be found for interpretation of shotgun proteomics data.