Computational and comparative proteogenomics : annotating genomes and proteomes using tandem mass spectrometry

Next generation sequencing techniques will soon lead to an explosive growth in the number of sequenced genomes and will turn manual gene and protein annotations into a luxury that can be afforded for only a small fraction of the newly sequenced genomes. In this work, we show that mass spectrometry can be a viable alternative high- throughput approach for accurate proteogenomic annotation. We present advances in statistical analysis of the reliability of peptide and protein identifications from mass spectrometry, and demonstrate how comparative analysis of multiple species or multiple experimental samples can provide additional insights for new biological discovery. We apply these approaches for correcting gene boundaries, discovering programmed frameshifts, N-terminal methionine cleavages, signal peptide cleavages and other in-vivo regulatory proteolytic events, post-translational modifications, analyzing specificity of individual proteases, detecting neuropeptides in brain tissue, and improving operon predictions. Based on this work, we recommend complementing genome sequencing projects by mass spectrometry-based proteogenomic