| With the rapid development of high throughput DNA sequencing, genomes of more and more species have been sequenced. Identifying and determining the structures of coding genes are the basic tasks of genome annotation. To understand the sequenced genome precisely, it is necessary to integrate muilti-"omics" data to annotate genomes. However, the annotation methods developed in the past decade are mainly based on genome and transcriptome data. Recently, mass spectrometry based proteomics has come of age, which can cover proteomes nearly completely and make it possible to use mass spectrometry data to annotate genomes. Mass spectrometry data can verify annotated genes on one hand, and refine annotated genes, discover novel genes on the other, which achieve the goal of re-annotating genomes. This is exactly the research content of proteogenomics, and using proteogenomic techniques to systematically annotate the sequenced genome is becoming increasingly important. This article reviews the research content, methods and recent trends of proteogenomics.