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.

The three-step procedure (Figure 1 ) utilizes in two first steps of MS/MS database searching, together with a standard determination of false positive detection rate (FDR), of which one search is conventional and another is a xeno-proteomics search for a foreign organism. On the third stage, label-free quantification is performed. First, the available proteomics MS/MS dataset is searched against the database of human protein sequences. All MS/MS spectra that fit to human sequences with a given FDR are then flagged. The remaining unassigned MS/MS spectra are then submitted to a second search, against a database of all known viral (or other foreign) proteins sequences. The presence of significant (in the FDR sense) matches indicates the presence of viral infection or contamination of the sample. The detected viral proteins are then quantified by one of the available label-free methods, and the proteins are ranked by their abundances. The rank of non-human proteins indicates the level of infection and the seriousness of its consequences for the cell.