title: Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.
abstract: Recent proliferation of low-cost DNA sequencing techniques will soon lead to an explosive growth in the number of sequenced genomes and will turn manual annotations into a luxury. Mass spectrometry recently emerged as a valuable technique for proteogenomic annotations that improves on the state-of-the-art in predicting genes and other features. However, previous proteogenomic approaches were limited to a single genome and did not take advantage of analyzing mass spectrometry data from multiple genomes at once. We show that such a comparative proteogenomics approach (like comparative genomics) allows one to address the problems that remained beyond the reach of the traditional "single proteome" approach in mass spectrometry. In particular, we show how comparative proteogenomics addresses the notoriously difficult problem of "one-hit-wonders" in proteomics, improves on the existing gene prediction tools in genomics, and allows identification of rare post-translational modifications. We therefore argue that complementing DNA sequencing projects by comparative proteogenomics projects can be a viable approach to improve both genomic and proteomic annotations.
authors.affiliation: Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA. ngupta@ucsd.edu
authors.forename: Nitin
authors.initials: N
authors.lastname: Gupta
authors.forename: Jamal
authors.initials: J
authors.lastname: Benhamida
authors.forename: Vipul
authors.initials: V
authors.lastname: Bhargava
authors.forename: Daniel
authors.initials: D
authors.lastname: Goodman
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Kain
authors.forename: Ian
authors.initials: I
authors.lastname: Kerman
authors.forename: Ngan
authors.initials: N
authors.lastname: Nguyen
authors.forename: Noah
authors.initials: N
authors.lastname: Ollikainen
authors.forename: Jesse
authors.initials: J
authors.lastname: Rodriguez
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
authors.forename: Margaret
authors.initials: M
authors.lastname: Romine
authors.forename: Vineet
authors.initials: V
authors.lastname: Bafna
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D016680:Genome, Bacterial; D023281:Genomics; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D040901:Proteomics; D017422:Sequence Analysis, DNA / Q000379:methods; D020614:Shewanella putrefaciens / Q000235:genetics; D053719:Tandem Mass Spectrometry / Q000379:methods