Genome annotation of Anopheles gambiae using mass spectrometry-derived data

Abstract

Background: A large number of animal and plant genomes have been completely sequenced over the last decade and are now publicly available. Although genomes can be rapidly sequenced, identifying protein-coding genes still remains a problematic task. Availability of protein sequence data allows direct confirmation of protein-coding genes. Mass spectrometry has recently emerged as a powerful tool for proteomic studies. Protein identification using mass spectrometry is usually carried out by searching against databases of known proteins or transcripts. This approach generally does not allow identification of proteins that have not yet been predicted or whose transcripts have not been identified.

Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation

“…MS has been extensively used for studying individual proteins; however, its application to whole genomes became feasible only recently with the arrival of efficient database search tools. Some groups have been successful in using MS/MS for improving gene predictions in newly sequenced organisms (Jaffe et al 2004a,b;Kalume et al 2005;Wang et al 2005), but there are no previous proteomic studies to obtain information about posttranslational processing (proteolysis, chemical modification) at whole proteome scale. Studies like those by Jaffe et al (2004a,b) that attempted to find PTMs at genome level had little or no success.…”

“…Church and colleagues used proteomic data for genome analysis of relatively small bacterium, Mycoplasma pneumoniae (Jaffe et al 2004a), and later on the newly sequenced Mycoplasma mobile, in which 26 genes were predicted exclusively based on proteomic data (Jaffe et al 2004b). Similar efforts have been made for other bacterial genomes (Kalume et al 2005;Wang et al 2005). Nevertheless, many significant technological challenges remain in using MS/MS for gene annotation, post-translational (proteolytic) processing, and modifications.…”

“…This study further develops the methods of proteogenomic annotations from Yates et al (1995), Kuster et al (2001), Oshiro et al (2002), Jaffe et al (2004a,b), Kalume et al (2005), , and Fermin et al (2006) and provides the first comprehensive analysis of post-translational modifications in complete genomes. Until very recently, such analysis was not feasible since the whole genome search for mutated and modified peptides was prohibitively time-consuming.…”

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

“…Comparative genomics analysis of multiple genomes has emerged as one of the key approaches for discovery of such genomic elements that greatly improves on the existing annotation tools (Batzoglou et al 2000;Kellis et al 2003;Xie et al 2005). Another recent development is the application of tandem mass spectrometry (MS/MS) for genomic annotations (Jaffe et al 2004;Kalume et al 2005;Wang et al 2005;Fermin et al 2006;Gupta et al 2007;Tanner et al 2007). Such proteogenomic approaches further improve gene predictions and allow one to address problems that remained beyond the reach of both traditional gene prediction tools and comparative genomics.…”

Expressed Peptide Tags: An Additional Layer of Data for Genome Annotation

“…17,[21][22][23][24][25][26][27][28] Arthur and Wilkins searched peptide mass fingerprints of 20 2D-gel spots from the extracellular matrix of Mycobacterium tuberculosis against a sixframe translation of the M. tuberculosis genome, mapped the peptides back to the genome, and identified regions with high concentration of peptide hits as coding regions. 22 They also demonstrated this strategy in limited application for a single human chromosome.…”