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

@article{gupta: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. 10.1101/gr.074344.107}, author = {Gupta, Nitin and Benhamida, Jamal and Bhargava, Vipul and Goodman, Daniel and Kain, Elisabeth and Kerman, Ian and Nguyen, Ngan and Ollikainen, Noah and Rodriguez, Jesse and Wang, Jian and Lipton, Mary S. and Romine, Margaret and Bafna, Vineet and Smith, Richard D. and Pevzner, Pavel A.}, citeulike-article-id = {2969076}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.074344.107}, citeulike-linkout-1 = {http://www.genome.org/cgi/content/abstract/18/7/1133}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18426904}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18426904}, day = {1}, doi = {10.1101/gr.074344.107}, journal = {Genome Res.}, keywords = {comparative, genomics, mass-spectrometry}, month = {July}, number = {7}, pages = {1133--1142}, posted-at = {2008-07-31 15:19:20}, priority = {2}, title = {Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes}, url = {http://dx.doi.org/10.1101/gr.074344.107}, volume = {18}, year = {2008} }

TY - JOUR ID - gupta:spectrometry L3 - citeulike-article-id:2969076 N2 - 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. 10.1101/gr.074344.107 IS - 7 JF - Genome Res. EP - 1142 TI - Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes VL - 18 SP - 1133 KW - comparative KW - genomics KW - mass-spectrometry AU - Gupta, Nitin AU - Benhamida, Jamal AU - Bhargava, Vipul AU - Goodman, Daniel AU - Kain, Elisabeth AU - Kerman, Ian AU - Nguyen, Ngan AU - Ollikainen, Noah AU - Rodriguez, Jesse AU - Wang, Jian AU - Lipton, Mary AU - Romine, Margaret AU - Bafna, Vineet AU - Smith, Richard AU - Pevzner, Pavel PY - 2008/07/01/ UR - http://dx.doi.org/10.1101/gr.074344.107 ER -