ArticleJournal of proteome research2016
Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy.
Article in Journal of proteome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Spritz: A Proteogenomic Database Engine.Journal of proteome research · 2021Article
- Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis.Computational and structural biotechnology journal · 2021Article
- Article
- Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements.Journal of proteome research · 2019Article
- Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks.Frontiers in plant science · 2019Review
- ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching.Journal of proteome research · 2018Article
- Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.Journal of proteome research · 2018Article
- Computational identification of micro-structural variations and their proteogenomic consequences in cancer.Bioinformatics (Oxford, England) · 2018Article
- Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys.BMC genomics · 2017Article
- Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.Genome medicine · 2017Article
- N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana.Molecular & cellular proteomics : MCP · 2017Article
- Global Post-Translational Modification Discovery.Journal of proteome research · 2017Article
- Post-translational modifications of FDA-approved plasma biomarkers in glioblastoma samples.PloS one · 2017Article
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5 authors.
Funding
Abstract
Mass-spectrometry-based proteomic analysis underestimates proteomic variation due to the absence of variant peptides and posttranslational modifications (PTMs) from standard protein databases. Each individual carries thousands of missense mutations that lead to single amino acid variants, but these are missed because they are absent from generic proteomic search databases. Myriad types of protein PTMs play essential roles in biological processes but remain undetected because of increased false discovery rates in variable modification searches. We address these two fundamental shortcomings of bottom-up proteomics with two recently developed software tools. The first consists of workflows in Galaxy that mine RNA sequencing data to generate sample-specific databases containing variant peptides and products of alternative splicing events. The second tool applies a new strategy that alters the variable modification approach to consider only curated PTMs at specific positions, thereby avoiding the combinatorial explosion that traditionally leads to high false discovery rates. Using RNA-sequencing-derived databases with this Global Post-Translational Modification (G-PTM) search strategy revealed hundreds of single amino acid variant peptides, tens of novel splice junction peptides, and several hundred posttranslationally modified peptides in each of ten human cell lines.
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