Author: Chernobrovkin, Alexey L.; Zubarev, Roman A.
Title: 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 Document date: 2014_3_11
ID: 0hrwqho8_30
Snippet: MaxQuant does not currently allow for two-stage database search procedure; therefore, MaxQuant quantification was based on the independent search of MS/MS spectra against a concatenated database containing both human and viral proteins. As expected, such a database search yielded many false positive viral identifications due to the overestimation of the a priori probabilities for viral peptides. In total, proteins corresponding to 75 viruses incl.....
Document: MaxQuant does not currently allow for two-stage database search procedure; therefore, MaxQuant quantification was based on the independent search of MS/MS spectra against a concatenated database containing both human and viral proteins. As expected, such a database search yielded many false positive viral identifications due to the overestimation of the a priori probabilities for viral peptides. In total, proteins corresponding to 75 viruses including different bacteriophages, murine coronavirus, tobacco mosaic virus, etc., have been ''identified'' by MaxQuant (Tables S5, S6, Figure S1 ). Such a gross overestimation of the viral proteins presence by searching in a concatenated database validates our two-stage database searching approach as most relevant.
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