ArticleMolecular & cellular proteomics : MCP2014
An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays.
Article in Molecular & cellular proteomics : MCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Improving the Genome Annotation ofCurrent genomics · 2021Article
- The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource.The Plant cell · 2021Article
- Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism inMicrobiology spectrum · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation.Plant physiology · 2020Article
- Combination of Proteogenomics with PeptidemBio · 2019Article
- The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling.Plant physiology · 2019Article
- Article
- Alternative splicing and translation play important roles in hypoxic germination in rice.Journal of experimental botany · 2019Article
- Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets.Molecular & cellular proteomics : MCP · 2019Article
- Computational identification of micro-structural variations and their proteogenomic consequences in cancer.Bioinformatics (Oxford, England) · 2018Article
- Multi-Omics Driven Assembly and Annotation of the Sandalwood (Plant physiology · 2018Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.Genome research · 2017Article
- Comparative Histological and Transcriptional Analysis of Maize Kernels Infected withFrontiers in plant science · 2017Article
- Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification.BMC genomics · 2016Article
- Systematic investigation of transcription factors critical in the protection against cerebral ischemia by Danhong injection.Scientific reports · 2016Article
- Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline.Molecular & cellular proteomics : MCP · 2016Article
- PGx: Putting Peptides to BED.Journal of proteome research · 2016Article
- An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.Molecular & cellular proteomics : MCP · 2016Article
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7 authors.
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Abstract
New technologies in genomics and proteomics have influenced the emergence of proteogenomics, a field at the confluence of genomics, transcriptomics, and proteomics. First generation proteogenomic toolkits employ peptide mass spectrometry to identify novel protein coding regions. We extend first generation proteogenomic tools to achieve greater accuracy and enable the analysis of large, complex genomes. We apply our pipeline to Zea mays, which has a genome comparable in size to human. Our pipeline begins with the comparison of mass spectra to a putative translation of the genome. We select novel peptides, those that match a region of the genome that was not previously known to be protein coding, for grouping into refinement events. We present a novel, probabilistic framework for evaluating the accuracy of each event. Our calculated event probability, or eventProb, considers the number of supporting peptides and spectra, and the quality of each supporting peptide-spectrum match. Our pipeline predicts 165 novel protein-coding genes and proposes updated models for 741 additional genes.
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