Tools to Co-visualize and Co-analyse Proteomic data with Genomes and Transcriptomes

Direct links between proteomic and genomic / transcriptomic data are not frequently made, partly due to lack of appropriate bioinformatics tools. To help address this, researchers at the University of New South Wales, Australia have developed the PG Nexus pipeline. The PG Nexus allow users to co-visualize peptides in the context of genomes or genomic contigs, along with RNA-seq reads. This is done in the Integrated Genome Viewer (IGV). A Results Analyser reports the precise base position where LC-MS/MS-derived peptides cover genes or gene isoforms, on the chromosomes or contigs where this occurs. In prokaryotes, the PG Nexus pipeline facilitates the validation of genes, where annotation or gene prediction is available, or the discovery of genes using a ‘virtual protein’-based unbiased approach. The researchers illustrate this with a comprehensive proteogenomics analysis of two strains of Campylobacter concisus. For higher eukaryotes, the PG Nexus facilitates gene validation and supports the identification of mRNA splice junction boundaries and splice variants that are protein-coding. This is illustrated with an analysis of splice junctions covered by human phosphopeptides, and other examples of relevance to the chromosome-centric Human Proteome Project.


Availability – The PG Nexus is open-source and available from It has been integrated into Galaxy and made available in the Galaxy tool shed.

  • Pang CN, Tay AP, Aya C, Twine NA, Harkness L, Hart-Smith G, Chia SZ, Chen Z, Deshpande NP, Kaakoush NO, Mitchell HM, Kassem M, Wilkins MR. (2013) Tools to Co-visualize and Co-analyse Proteomic data with Genomes and Transcriptomes: validation of genes and alternative mRNA splicing. J Proteome Res [Epub ahead of print]. [abstract]