ArticleGenome research2007
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
96 citing papers in PubMed, 192 citations in OpenAlex.
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- Graphene nano-electromechanical mass sensor with high resolution at room temperature.iScience · 2023Article
- Identification of Novel Genes and Proteoforms inPathogens (Basel, Switzerland) · 2022Article
- "Pseudo-pseudogenes" in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica.Nucleic acids research · 2022Article
- Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry.iScience · 2022Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Fast Sampling of the Cellular Metabolome.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance.BMC microbiology · 2021Article
- Can proteomics-based approaches further help COVID-19 prevention and therapy?Expert review of proteomics · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- The Experimental Proteome ofGenes · 2020Article
- Beyond mass spectrometry, the next step in proteomics.Science advances · 2020Review
- Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.Genome biology and evolution · 2018Article
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.Genome research · 2017Article
- Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu.Biochemistry · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.Molecular & cellular proteomics : MCP · 2016Article
- The omic approach to parasitic trematode research-a review of techniques and developments within the past 5 years.Parasitology research · 2016Review
36 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.
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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.