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.

HEK293 cell line has been established by transformation of normal human embryonic kidney cells with sheared DNA of adenovirus 5 and it is known to express viral proteins E1A and E1B [34] . The HEK293 proteome, as well as the other 10 proteomes in the cited study [18] , was represented by 620,000620,000 MS/MS spectra obtained from the authors. The first-stage search on HEK293 proteome by Mascot (MatrixScience, UK) attributed 361,736 of the 624,107 MS/MS spectra to human-originated tryptic peptides. The search results were rescored by Percolator and filtered at 1% FDR, yielding 7,970 human protein groups. The remained spectra were searched against the viral subset of the SwissProt database using a Mascot feature ''re-search non-significant spectra''. The results were processed by Percolator as above, yielding three proteins (E1BS, E1BL and E1A) of human adenovirus 5 (Table S1 ). Using intensity-based label-free quantification, we estimated the relative abundance of viral proteins compared to the human cellular proteome (Table S2 ). E1BS and E1BL proteins were found to be among the top 100 most abundant proteins expressed by HEK293 cells. Thus, viral proteins can't be ignored when doing even most ''shallow'' proteomics work. With this example, we established that our procedure successfully detects viral proteins that should be present in the cell ''by design''.