{
  "abstract": "Endogenous peptides represent a rich source of bioactive molecules that regulate diverse physiological processes and offer opportunities for functional discovery. Mass spectrometry-based peptidomics enables their systematic characterization, yet public datasets remain fragmented and are often processed using heterogeneous tools and parameters, limiting peptide-level retrieval, cross-study exploration, and data reuse. We developed PeptidomicsDB (freely accessible at http://www.inbirg.com/ppd/), a unified resource based on the standardized reanalysis of 151 public peptidomics projects comprising 3992 biological samples from major branches, including global peptidomics, neuropeptidomics, and immunopeptidomics, across species and biological contexts. Using the DeepNovo Peptidome workflow implemented in PEAKS Studio 13.0, which integrates database searching, homology searching, and de novo sequencing, we identified >33 million peptide records representing over 4 million unique peptide sequences, of which >400 000 showed sequence similarity to bioactive peptides curated in public repositories. Analysis of 249 curated pairwise comparison datasets identified 78 910 differentially abundant peptide records, while 14 context-specific datasets yielded 148 175 peptide records enriched in individual tissues, diseases, or cell types. PeptidomicsDB links peptide, precursor-protein, sample, and dataset levels with experimental provenance, quantitative evidence, mass spectrometric data, and functional annotations. Together, these capabilities support peptide discovery and functional exploration.",
  "abstract_shown": true,
  "affiliations": [
    "Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, College of Pharmacy, Chongqing Medical University , Chongqing 400016 ,",
    "The First Clinical College of Chongqing Medical University , Chongqing 400016 ,",
    "Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016 ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Fengyuan Yang"
    },
    {
      "affs": [
        0
      ],
      "name": "Yichen Guo"
    },
    {
      "affs": [
        0
      ],
      "name": "Peiqi Luo"
    },
    {
      "affs": [
        0
      ],
      "name": "Yucheng Wu"
    },
    {
      "affs": [
        0
      ],
      "name": "Yapeng Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Zishun Zhang"
    },
    {
      "affs": [
        0
      ],
      "name": "Na Ge"
    },
    {
      "affs": [
        1
      ],
      "name": "Haihan Yuan"
    },
    {
      "affs": [
        0
      ],
      "name": "Desi Liu"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Jianbo Pan",
      "orcid": "0000-0001-6014-8160"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3e010a5z57rbn.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag1032",
  "fulltext_url": null,
  "id": "3e010a5z57rbn",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1032/8986579",
  "language": null,
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1607|Advanced Proteomics Techniques and Applications"
    ]
  ],
  "openalex": "W7223376548",
  "pdf_url": "https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkag1032/72410659/gkag1032.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-23",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/3e010a5z57rbn.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:50Z",
      "native_id": "10.1093/nar/gkag1032",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1032/8986579"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1607|Advanced Proteomics Techniques and Applications",
      "subfield": "physical"
    }
  ],
  "title": "PeptidomicsDB: a unified resource of endogenous peptidomes for peptide discovery and functional exploration across species and biological contexts",
  "title_text": "PeptidomicsDB: a unified resource of endogenous peptidomes for peptide discovery and functional exploration across species and biological contexts",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:50Z",
  "url": "https://research.draconitic.com/paper/3e010a5z57rbn",
  "venue": "Nucleic Acids Research",
  "versions": []
}