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
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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1415482"], "description"=>"<p>(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.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein classes", "biotechnology", "microbiology", "Virology", "Viral classification", "Viral enzymes", "Model organisms", "proteomics", "Protein abundance", "Spectrometric identification of proteins", "Infectious diseases", "Viral diseases", "suggested", "three-step", "workflow", "shotgun", "includes"], "article_id"=>958292, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Alexey L. Chernobrovkin", "Roman A. Zubarev"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091433.g001", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_suggested_three_step_workflow_of_shotgun_proteomics_analysis_that_includes_contamination_infection_detection_/958292", "title"=>"The suggested three-step workflow of shotgun proteomics analysis that includes contamination/infection detection.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-11 03:24:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1415487"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein classes", "biotechnology", "microbiology", "Virology", "Viral classification", "Viral enzymes", "Model organisms", "proteomics", "Protein abundance", "Spectrometric identification of proteins", "Infectious diseases", "Viral diseases", "xmrv", "viral", "proteome"], "article_id"=>958297, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Alexey L. Chernobrovkin", "Roman A. Zubarev"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091433.g002", "stats"=>{"downloads"=>4, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_levels_of_the_XMRV_viral_proteins_within_the_proteome_of_the_human_cell_line_LNCaP_/958297", "title"=>"Expression levels of the XMRV viral proteins within the proteome of the human cell line LNCaP.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-11 03:24:00"}

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Relative Metric

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