ArticleMolecular & cellular proteomics : MCP2013
Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.
Article in Molecular & cellular proteomics : MCP, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 42 citations in OpenAlex.
- Advances in Decoding Bacterial N-Terminal Proteoforms: Technologies, Challenges, and Functional Insights.Microorganisms · 2026Review
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.Genome research · 2017Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- Article
- GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.Molecular & cellular proteomics : MCP · 2016Article
- Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline.Molecular & cellular proteomics : MCP · 2016Article
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- Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation.Molecular & cellular proteomics : MCP · 2016Article
- PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.Bioinformatics (Oxford, England) · 2014Article
- A proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixA locus for symbiosis.International journal of molecular sciences · 2014Article
- The bacterial proteogenomic pipeline.BMC genomics · 2014Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present GenoSuite, an integrated proteogenomic pipeline to validate, refine and discover protein coding genes using high-throughput mass spectrometry (MS) data from prokaryotes. To demonstrate the effectiveness of GenoSuite, we analyzed proteomics data of Bradyrhizobium japonicum (USDA110), a model organism to study agriculturally important rhizobium-legume symbiosis. Our analysis confirmed 31% of known genes, refined 49 gene models for their translation initiation site (TIS) and discovered 59 novel protein coding genes. Notably, a novel protein which redefined the boundary of a crucial cytochrome P450 system related operon was discovered, known to be highly expressed in the anaerobic symbiotic bacteroids. A focused analysis on N-terminally acetylated peptides indicated downstream TIS for gene blr0594. Finally, ortho-proteogenomic analysis revealed three novel genes in recently sequenced B. japonicum USDA6(T) genome. The discovery of large number of missing genes and correction of gene models have expanded the proteomic landscape of B. japonicum and presents an unparalleled utility of proteogenomic analyses and versatility of GenoSuite for annotating prokaryotic genomes including pathogens.
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