Mining Proteomics Datasets to Uncover Functional Pseudogenes

Abstract

Analysis of the proteome, combined with the human genome sequence, improved gene annotation and confirmed that some genes are actually expressed as proteins, including pseudogenes, alternative reading frames, and additional protein isoforms. Although sequencing a genome is a challenge in itself, the annotation of all genes encoding proteins is a bigger one. Here, we describe an in silico approach to identify evidence of pseudogene expression, as well as an experimental approach for the validation of the protein encoded by pseudogenes, including the steps necessary to quantify these proteins. This technique enables a comprehensive analysis for the expression of genes into proteins that were not suspected of existing.

Keywords: Mass spectrometry; Parallel reaction monitoring; Protein expression; Proteomics; Pseudogenes.