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.

Mass-spectrometric data (raw data files) were provided: deep proteomics of eleven common cell lines [18] by Mann's group (data were deposited at ProteomeCommons.org Tranche); sixty proteome datasets for NCI-60 cancer cell lines -by Kuster's group [29] (data can now be downloaded from the web http://wzw.tum. de/proteomics/nci60). Both datasets comprise mass-spectra obtained from the whole cell lysates. Proteins were extracted from cells, digested with trypsin. Peptide mixtures where separated using 1D (reverse-phase liquid chromatography) or 2D protocol (strong cation exchange chromatography followed by reversephase liquid chromatography). Mass-spectra were acquired in data-dependent mode with CID or HCD fragmentation. MS 2 spectra were extracted and stored in Mascot generic file (mgf) format using in-house developed Raw2MGF software (available for non-commercial use upon request), with peak picking performed using Thermo Xcalibur centroiding. No filtering or preprocessing of raw MS/MS data was performed. For each cell line, a single mgf file containing all available MS/MS spectra was produced manually by concatenation of individual LC/MS data files. [30] , which makes it representative but non-redundant protein sequence database.