ArticleGenome research2008
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Article
- Article
- Article
- Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.Genome research · 2017Article
- SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.Journal of proteome research · 2016Article
- Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu(2+) Treatment.Frontiers in microbiology · 2016Article
- Mechanism study of peptide GMBP1 and its receptor GRP78 in modulating gastric cancer MDR by iTRAQ-based proteomic analysis.BMC cancer · 2015Article
- Article
- The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.Scientific data · 2015Article
- Proteogenomics: concepts, applications and computational strategies.Nature methods · 2014Review
- Systems biology perspectives on minimal and simpler cells.Microbiology and molecular biology reviews : MMBR · 2014Review
- An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays.Molecular & cellular proteomics : MCP · 2014Article
- Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.Molecular & cellular proteomics : MCP · 2013Article
- Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans.International journal of proteomics · 2013Article
- Article
- Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies.Journal of proteome research · 2012Article
- Protein identification using top-down.Molecular & cellular proteomics : MCP · 2012Article
- High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade.BMC genomics · 2012Article
- Computational approaches to protein inference in shotgun proteomics.BMC bioinformatics · 2012Review
- Article
Corrections and comments
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Authors and funding
15 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.