Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.
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.
Gupta
Nitin
N
Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA. ngupta@ucsd.edu
Benhamida
Jamal
J
Bhargava
Vipul
V
Goodman
Daniel
D
Kain
Elisabeth
E
Kerman
Ian
I
Nguyen
Ngan
N
Ollikainen
Noah
N
Rodriguez
Jesse
J
Wang
Jian
J
Lipton
Mary S
MS
Romine
Margaret
M
Bafna
Vineet
V
Smith
Richard D
RD
Pevzner
Pavel A
PA
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