ArticleProteomics2014
A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites.
Article in Proteomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Advances in Decoding Bacterial N-Terminal Proteoforms: Technologies, Challenges, and Functional Insights.Microorganisms · 2026Review
- Microproteins in Metabolic Biology: Emerging Functions and Potential Roles as Nutrient-Linked Biomarkers.International journal of molecular sciences · 2025Review
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Eukaryotic Microproteins.Annual review of biochemistry · 2025Review
- Comprehensive discovery and functional characterization of the noncanonical proteome.Cell research · 2025Article
- Evaluation of Eukaryotic mRNA Coding Potential.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- Microproteins-Discovery, structure, and function.Proteomics · 2023Review
- What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?Molecular & cellular proteomics : MCP · 2023Article
- N-terminal proteoforms may engage in different protein complexes.Life science alliance · 2023Article
- What can Ribo-seq and proteomics tell us about the non-canonical proteome?bioRxiv : the preprint server for biology · 2023Article
- Review
- Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID.Molecular cell · 2022Article
- Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor.Nature chemical biology · 2022Article
- Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures.Journal of biomedical science · 2022Review
- Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Analysis of herbivore-responsive long noncoding ribonucleic acids reveals a subset of small peptide-coding transcripts inFrontiers in plant science · 2022Article
- Extensive Translational Regulation through the Proliferative Transition of Trypanosoma cruzi Revealed by Multi-Omics.mSphere · 2021Article
- Noncanonical open reading frames encode functional proteins essential for cancer cell survival.Nature biotechnology · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
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Authors and funding
13 authors.
Funding
Abstract
Next-generation transcriptome sequencing is increasingly integrated with MS to enhance MS-based protein and peptide identification. Recently, a breakthrough in transcriptome analysis was achieved with the development of ribosome profiling (ribo-seq). This technology is based on the deep sequencing of ribosome-protected mRNA fragments, thereby enabling the direct observation of in vivo protein synthesis at the transcript level. In order to explore the impact of a ribo-seq-derived protein sequence search space on MS/MS spectrum identification, we performed a comprehensive proteome study on a human cancer cell line, using both shotgun and N-terminal proteomics, next to ribosome profiling, which was used to delineate (alternative) translational reading frames. By including protein-level evidence of sample-specific genetic variation and alternative translation, this strategy improved the identification score of 69 proteins and identified 22 new proteins in the shotgun experiment. Furthermore, we discovered 18 new alternative translation start sites in the N-terminal proteomics data and observed a correlation between the quantitative measures of ribo-seq and shotgun proteomics with a Pearson correlation coefficient ranging from 0.483 to 0.664. Overall, this study demonstrated the benefits of ribosome profiling for MS-based protein and peptide identification and we believe this approach could develop into a common practice for next-generation proteomics.
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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.