Reconciling proteomics with next generation sequencing

• Multi-omics integration is important for thorough understanding of biology.
• NGS is a powerful technique to interface genomics with proteomics–proteogenomics.
• DNAseq, RNAseq and RIBOseq improve proteoform identification and discrimination.
• NGS and proteomics data need to be cross-evaluated critically by different omics communities.
• The main objective in multi-omics integration is to quantitatively correlate phenotypes to relevant genotypes.

Both genomics and proteomics technologies have matured in the last decade to a level where they are able to deliver system-wide data on the qualitative and quantitative abundance of their respective molecular entities, that is DNA/RNA and proteins. A next logical step is the collective use of these technologies, ideally gathering data on matching samples. The first large scale so-called proteogenomics studies are emerging, and display the benefits each of these layers of analysis has on the other layers to together generate more meaningful insight into the connection between the phenotype/physiology and genotype of the system under study. Here we review a selected number of these studies, highlighting what they can uniquely deliver. We also discuss the future potential and remaining challenges, from a somewhat proteome biased perspective.

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