Proteogenomics integrates two different research fields, mass spectrometry (MS) based proteomics and next-generation sequencing (NGS) based genomics, transcriptomics, or translatomics. In this review we aimed at sketching a comprehensive overview of all the bioinformatics solutions that are available for this growing research area. Some of these are presented as stand-alone solutions, whereas others are implemented in a web-based framework such as Galaxy. Over the last few years a handful integrative tools also became available that can execute complete proteogenomics analyses. building custom sequence databases (based on next generation sequencing output) for mass spectrometry fragmentation spectrum matching. Some of these solutions only help in specific steps of the proteogenomics studies, e.g. Over the years, a growing amount of bioinformatics tools and databases became available to help streamlining these cross-omics studies. Other proteogenomics studies using a combination of proteomics and genomics techniques focus on antibody sequencing, the identification of immunogenic peptides or venom peptides. Also, the identification of novel proteoforms is also made possible based on detection of novel translation initiation sites (cognate or near-cognate), novel transcript isoforms, sequence variation or novel (small) open reading frames in intergenic or un-translated genic regions by analyzing high-throughput sequencing data from RNAseq or ribosome profiling experiments. Mass spectrometry based identifications of matching or homologues peptides can further refine gene models.

Currently, the main goals of the field are to aid genome annotation or to unravel the proteome complexity. Proteogenomics is a research area that combines areas as proteomics and genomics in a multi-omics setup using both mass spectrometry and high-throughput sequencing technologies.

Nokoi peptideshaker