ArticleGenome research2019
PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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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
70 citing papers in PubMed, 109 citations in OpenAlex.
- Article
- A Viral Mutation Profiling and Discovery Strategy for Sensitive Multiplex Detection of Viruses and Variants in Saliva by Proteomics.bioRxiv : the preprint server for biology · 2026Article
- Assessing the Performance of Mass Spectrometry Search Strategies in Identifying Translational Errors Using PDX Proteomics Data.Molecular & cellular proteomics : MCP · 2026Article
- Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics.Nature communications · 2026Article
- Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.Journal of proteomics · 2026Article
- ImmunoPepper: extracting personalized peptides from complex splicing graphs.Bioinformatics (Oxford, England) · 2026Article
- IPScan: Detecting novel intronic PolyAdenylation events with RNA-seq data.PLoS computational biology · 2025Article
- Alternate RNA decoding results in stable and abundant proteins in mammals.bioRxiv : the preprint server for biology · 2025Article
- Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues.Nucleic acids research · 2025Article
- Potential shared neoantigens from pan-cancer transcript isoforms.Scientific reports · 2025Article
- Open-Source and FAIR Research Software for Proteomics.Journal of proteome research · 2025Review
- PepCentric Enables Fast Repository-Scale Proteogenomics Searches.bioRxiv : the preprint server for biology · 2025Article
- Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.Scientific reports · 2025Article
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.Journal of the American Society for Mass Spectrometry · 2024Article
- Detection of host cell microprotein impurities in antibody drug products.Nature communications · 2024Article
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- NCI's Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data.Cancer research communications · 2024Article
- Article
- Article
10 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
3 authors at 1 institution in 1 country.
Funding
Abstract
Massively parallel or second-generation sequencing-based genomic studies continuously identify new genomic alterations that may lead to novel protein sequences, which are attractive candidates for disease biomarkers and therapeutic targets after proteomic validation. Integrative proteogenomic methods have been developed to use mass spectrometry (MS)-based proteomics data for such validation. These methods replace the reference sequence database in proteomic database searching with a customized protein database that incorporates sample- or disease-specific sequences derived from DNA or RNA sequencing, thus enabling the identification of novel protein sequences. Although useful, this spectrum-centric approach requires a full evaluation of all possible spectrum-peptide pairs, which is time-consuming, error-prone, and difficult to apply. Here, we present PepQuery, a peptide-centric approach that focuses on only novel DNA or protein sequences of interest. PepQuery allows quick and easy proteomic validation of genomic alterations without customized database construction. We demonstrated the sensitivity and specificity of the approach in validating completely novel proteins, novel splice junctions, and single amino acid variants using simulations and experimental data. Notably, enabling unrestricted modification searching in PepQuery reduced false positives by up to 95%. We implemented PepQuery as both web-based and stand-alone applications. The web version provides direct access to more than half a billion MS/MS spectra from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and other cancer proteomic studies. The stand-alone version supports batch analysis and user-provided MS/MS data. PepQuery will increase the usage of proteogenomics beyond the proteomics community and will broaden the application of proteogenomics in personalized medicine.
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What OpenQuestion holds
Registered trials
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.