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. Currently, the main goals of the field are to aid 
genome annotation or to unravel the proteome complexity. Mass spectrometry based 
identifications of matching or homologues peptides can further refine gene 
models. 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. 
Other proteogenomics studies using a combination of proteomics and genomics 
techniques focus on antibody sequencing, the identification of immunogenic 
peptides or venom peptides. Over the years, a growing amount of bioinformatics 
tools and databases became available to help streamlining these cross-omics 
studies. Some of these solutions only help in specific steps of the 
proteogenomics studies, e.g. building custom sequence databases (based on next 
generation sequencing output) for mass spectrometry fragmentation spectrum 
matching. Over the last few years a handful integrative tools also became 
available that can execute complete proteogenomics analyses. Some of these are 
presented as stand-alone solutions, whereas others are implemented in a 
web-based framework such as Galaxy. In this review we aimed at sketching a 
comprehensive overview of all the bioinformatics solutions that are available 
for this growing research area. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 
36:584-599, 2017.