ArticleMolecular & cellular proteomics : MCP2016
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 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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Who cites it
64 citing papers in PubMed.
- High-Rate Fingerprinting of Protein Isoforms by Quasi-regulated Enzyme-free Transport Through CytK Nanopores.Research square · 2026Article
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
- Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples.Cell reports methods · 2026Article
- ImmunoPepper: extracting personalized peptides from complex splicing graphs.Bioinformatics (Oxford, England) · 2026Article
- Protein Sequencing with Single Amino Acid Resolution Discerns Peptides That Discriminate Tropomyosin Proteoforms.Journal of proteome research · 2025Article
- Identification of non-canonical peptides with moPepGen.bioRxiv : the preprint server for biology · 2025Article
- Article
- HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy.Cell · 2025Article
- Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants.Proteomes · 2024Article
- Parsing 20 Years of Public Data by AI Maps Trends in Proteomics and Forecasts Technology.Journal of proteome research · 2024Review
- Comparative RNA-Seq Analysis Revealed Tissue-Specific Splicing Variations during the Generation of the PDX Model.International journal of molecular sciences · 2023Article
- Article
- Article
- OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases.Journal of proteome research · 2023Article
- PepQuery2 democratizes public MS proteomics data for rapid peptide searching.Nature communications · 2023Article
- Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues.Nature communications · 2023Article
- Variant biomarker discovery using mass spectrometry-based proteogenomics.Frontiers in aging · 2023Review
- Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways.Cell reports. Medicine · 2022Article
- Cancer proteogenomics: current impact and future prospects.Nature reviews. Cancer · 2022Review
- Therapeutic Vaccines Targeting Neoantigens to Induce T-Cell Immunity against Cancers.Pharmaceutics · 2022Review
4 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
38 authors.
Funding
Abstract
Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNVs without a detectable mRNA transcript were also observed, suggesting that transcriptome coverage was incomplete (∼80%). In contrast to germline variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than in the luminal tumor, raising the possibility of differential translation or protein degradation effects. In conclusion, this large-scale proteogenomic integration allowed us to determine the degree to which mutations are translated and identify gaps in sequence coverage, thereby benchmarking current technology and progress toward whole cancer proteome and transcriptome analysis.
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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.