ArticleGenome research2009
Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Selective profiling of liver-related specific proteins based on sofosbuvir-modified magnetic separation material.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2023Article
- Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications inFrontiers in microbiology · 2022Article
- Comprehensive Comparative Analysis of Cholesterol Catabolic Genes/Proteins in Mycobacterial Species.International journal of molecular sciences · 2019Article
- N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana.Molecular & cellular proteomics : MCP · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- Sharpening Host Defenses during Infection: Proteases Cut to the Chase.Molecular & cellular proteomics : MCP · 2017Review
- Peptides Labeled with Pyridinium Salts for Sensitive Detection and Sequencing by Electrospray Tandem Mass Spectrometry.Scientific reports · 2016Article
- Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias.Microbial genomics · 2016Article
- Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline.Molecular & cellular proteomics : MCP · 2016Article
- Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry.Frontiers in microbiology · 2016Article
- Proteomic tools to decipher microbial community structure and functioning.Environmental science and pollution research international · 2015Review
- Dual use of peptide mass spectra: Protein atlas and genome annotation.Current plant biology · 2015Article
- Systems Biology Approaches to Understand Natural Products Biosynthesis.Frontiers in bioengineering and biotechnology · 2015Review
- Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1.Frontiers in microbiology · 2015Article
- Identification of protein N-termini using TMPP or dimethyl labeling and mass spectrometry.Methods in molecular biology (Clifton, N.J.) · 2015Article
- The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.Scientific data · 2015Article
- Mycobacterial tlyA gene product is localized to the cell-wall without signal sequence.Frontiers in cellular and infection microbiology · 2015Article
- Toward a standard in structural genome annotation for prokaryotes.Standards in genomic sciences · 2015Article
- Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods.Molecular & cellular proteomics : MCP · 2014Article
- Potential cross-reactivity of monoclonal antibodies against clinically relevant mycobacteria.Clinical and experimental immunology · 2014Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The progress in sequencing technologies irrigates biology with an ever-increasing number of genome sequences. In most cases, the gene repertoire is predicted in silico and conceptually translated into proteins. As recently highlighted, the predicted genes exhibit frequent errors, particularly in start codons, with a serious impact on subsequent biological studies. A new "ortho-proteogenomic" approach is presented here for the annotation refinement of multiple genomes at once. It combines comparative genomics with an original proteomic protocol that allows the characterization of both N-terminal and internal peptides in a single experiment. This strategy was applied to the Mycobacterium genus with Mycobacterium smegmatis as the reference, and identified 946 distinct proteins, including 443 characterized N termini. These experimental data allowed the correction of 19% of the characterized start codons, the identification of 29 proteins missed during the annotation process, and the curation, thanks to comparative genomics, of 4328 sequences of 16 other Mycobacterium proteomes.
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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.