Proteogenomics 101: a primer on database search strategies

Proteogenomics refers to the integration of high-throughput genomics/transcriptomics with proteomics data for genome annotation, novel gene discovery, and variant peptide detection to facilitate the discovery of novel proteoforms and insights into disease biology. The novel proteoforms revealed by proteogenomics can lead to a better understanding of important biological processes, discovery of novel cellular regulators, and new therapeutic targets. While proteogenomics approaches have demonstrated extensive applications in biological research, their implementation remains challenging due to the requirement of sophisticated tools and pipelines to conduct the multitude of steps successfully. Here, we provide a bird’s eye view of these steps, methods, and tools that help achieve the desired goals. For researchers who wish to dive into proteogenomics, this review will act as a quick start guide enumerating the steps, their use cases, applications, and appropriate tools for the given purpose. This includes custom database construction, database searches, detecting non-canonical peptides, controlling false discovery rate (FDR), analysis, and visualization. This review aims to introduce proteogenomics to researchers new to the domain and help them achieve novel insights into biological processes, deeper knowledge on disease biology, and discovery of potential therapeutic targets.