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

TitleComparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.
Publication TypeJournal Article
Year of Publication2008
AuthorsGupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA
JournalGenome Res
Volume18
Issue7
Pagination1133-42
Date Published2008 Jul
ISSN1088-9051
KeywordsAmino Acid Sequence, Base Sequence, Genome, Bacterial, Genomics, Mass Spectrometry, Molecular Sequence Data, Proteomics, Sequence Analysis, DNA, Shewanella putrefaciens, Tandem Mass Spectrometry
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.

DOI10.1101/gr.074344.107
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/18426904?dopt=Abstract
PMCPMC2493402
Alternate TitleGenome Res.
PubMed ID18426904