iPRG-2013 Proteome Informatics Research Group study: Using RNA-seq data to refine proteomic data analysis

Abstract

The Proteome Informatics Research Group (iPRG) this year performed a study to evaluate the benefits of using databases derived from RNA-Seq data for peptide identification. The proteomic dataset provided consisted of high mass accuracy tandem mass spectra acquired when analyzing human peripheral blood mononuclear cells. A variety of different types of sequence databases were supplied. These included a standard protein sequence database; a database containing only sequences of proteins expressed in the sample based on RNA-Seq data; a database that included sequence and splice variants; a database of sequences that could not be reconciled to known expressed gene sequences. Participants were asked to report spectral identifications in the form of an Excel spreadsheet, highlighting those identifications that were only identified using one of the RNA-Seq derived specialized sequence databases. Participants were also required to complete a web-based questionnaire summarizing the tools and methods they used. Additional peptide identifications were achieved by the use of each of the different RNA-Seq derived databases, although the number of additional identifications was modest. Nevertheless, these new identifications could have potential biological significance, so this type of analysis may still be worthwhile