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 - PubMed (original) (raw)

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

Alexey L Chernobrovkin et al. PLoS One. 2014.

Abstract

Cell cultures used routinely in proteomic experiments may contain proteins from other species because of infection, transfection or just contamination. Since infection or contamination may affect the results of a biological experiment, it is important to test the samples for the presence of "alien" proteins. Usually cells are tested only for the most common infections, and most of the existing tests are targeting specific contaminations. Here we describe a three-step procedure for reliable untargeted detection of viral proteins using proteomics data, and recommend this or similar procedure to be applied to every proteomics dataset submitted for publication.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. The suggested three-step workflow of shotgun proteomics analysis that includes contamination/infection detection.

(1) conventional matching the experimental MS/MS spectra against the protein database of the host organism (human); (2) Unmatched MS/MS spectra and insignificant matches in terms of FDR are matched against viral protein database. (3) The presence of significant hits at the second step points to the potential infection/contamination of the sample. Label-free quantitative analysis of identified proteins (both host and contaminant) provides an estimation of the contamination level and thus severity of the problem.

Figure 2

Figure 2. Expression levels of the XMRV viral proteins within the proteome of the human cell line LNCaP.

Small red dots correspond to the host cell proteins, whereas the two identified viral proteins are marked as cyan circles. Detected sequences of tryptic peptides of the two viral proteins are marked with color: red - peptides mapped perfectly on the XMRV sequence; blue and green - mutated sequences.

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