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.

An opposite extreme is to ignore the host sequences in the proteomics data and focus on the viral ones, thus assigning zero a priori probability to host proteins and 100% -to viral proteins. Such an approach was utilized by Bromenshenk et al. [21] , which resulted in their identifying peptides of Iridovirus and Nosema origin in North American honey bees. However, subsequent studies by Foster [22] and Knudsen and Chalkley [23] have proved findings of Bromenshenk et al. wrong, with the misidentification of viral proteins being caused by inappropriate usage of viral-only sequence database for mass-spectrometry data interpretation. In human proteomics, false positive identification of viral peptides is even more likely in the above approach given that up to 8% of human genome has viral origin [24, 25] , and thus some human proteins exhibit high degree of homology to retroviral proteins.