ArticleNature communications2023
PepQuery2 democratizes public MS proteomics data for rapid peptide searching.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed, 42 citations in OpenAlex.
- pAnno: a comprehensive, precise, and fast proteogenomic workflow for the discovery of novel coding regions.Genome biology · 2026Article
- A Proteogenomic Approach to Discover Novel lncRNA-Derived Microproteins and Their Potential Clinical Utility in Hepatocellular Carcinoma.Molecular & cellular proteomics : MCP · 2026Article
- Short SCN5A Transcript Yields a NaV1.5 Fragment Influencing Cardiac Metabolism.Circulation research · 2026Article
- Integration of Short- and Long-Read RNA Sequencing Enables the Discovery of Circular RNAs.Cancer research · 2026Article
- iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.Genome biology · 2026Article
- Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.Journal of proteomics · 2026Article
- Article
- A Citrate Synthase Splice Variant Rewires the TCA Cycle to Promote Colorectal Cancer Progression.Cancer research · 2025Article
- Alternative splicing generates HER2 isoform diversity underlying antibody-drug conjugate resistance in breast cancer.Genome research · 2025Article
- High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.bioRxiv : the preprint server for biology · 2025Article
- TopLib: Building and Searching Top-Down Mass Spectral Libraries for Proteoform Identification.Analytical chemistry · 2025Article
- PepCentric Enables Fast Repository-Scale Proteogenomics Searches.bioRxiv : the preprint server for biology · 2025Article
- Noncanonical altPIDD1 protein: unveiling the true major translational output of theLife science alliance · 2025Article
- Article
- 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
- Article
- Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart.Journal of proteome research · 2024Article
- A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.mSphere · 2024Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We present PepQuery2, which leverages a new tandem mass spectrometry (MS/MS) data indexing approach to enable ultrafast, targeted identification of novel and known peptides in any local or publicly available MS proteomics datasets. The stand-alone version of PepQuery2 allows directly searching more than one billion indexed MS/MS spectra in the PepQueryDB or any public datasets from PRIDE, MassIVE, iProX, or jPOSTrepo, whereas the web version enables users to search datasets in PepQueryDB with a user-friendly interface. We demonstrate the utilities of PepQuery2 in a wide range of applications including detecting proteomic evidence for genomically predicted novel peptides, validating novel and known peptides identified using spectrum-centric database searching, prioritizing tumor-specific antigens, identifying missing proteins, and selecting proteotypic peptides for targeted proteomics experiments. By putting public MS proteomics data directly into the hands of scientists, PepQuery2 opens many new ways to transform these data into useful information for the broad research community.
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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.