{
  "abstract": "Deciphering the functions of post-translational modifications (PTMs) is a critical bridge connecting large-scale modification proteomics data to mechanistic studies. However, most existing tools for visualizing PTM omics data are limited to site catalogs or single-dimensional feature displays. They lack the capability to simultaneously map user-derived differential modification sites onto multi-dimensional contexts, including protein three-dimensional (3D) structure, evolutionary conservation, functional sites, and disease associations. This limitation makes it difficult for researchers to rapidly assess the biological importance of candidate sites from among a vast number of differentially modified sites. Here, we present PTMExplorer, an interactive platform for the multi-dimensional visualization of protein PTMs. PTMExplorer comprises three core modules: PTM Inspector, built upon ProtVista, provides a multi-track, sequence-feature integrated view incorporating intrinsically disordered region (IDR) prediction (via flDPnn), surface accessibility calculation (via FreeSASA), and UniProt functional annotations; PTM 3D Locator, leveraging the Nightingale/Mol* engine, anchors modification sites onto AlphaFold/Protein Data Bank (PDB) 3D structures through residue mapping via PDBe-SIFTS; and PTM Overview, utilizing the R circlize package, presents a panoramic polar circos plot illustrating modification distribution and inter-group differential regulation. Additionally, three major disease-associated modification databases (PTMD, qPTM, and PhosCancer) are integrated as PTM-Disease Nexus, enabling co-localization comparison between user-defined differential sites and reported disease-related sites. PTMExplorer currently supports eight model organisms, accepts user-uploaded differential analysis results, and provides multi-dimensional annotations and various visualization options (https://www.bioladder.cn/PTMExplorer/). Using a multi-omics dataset from hepatocellular carcinoma (18 patients, 9 modification types) as a case study, we demonstrate the practical utility of PTMExplorer in screening potential biomarkers, revealing multi-modification coordination mechanisms, and distinguishing between absolute and relative quantification patterns.",
  "abstract_shown": true,
  "affiliations": [
    "Beijing Qinglian Biotech Co., Ltd"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "name": "C. Li"
    },
    {
      "name": "J. Wang"
    },
    {
      "name": "C. He"
    },
    {
      "name": "H. Wang"
    },
    {
      "name": "S. Geng"
    },
    {
      "name": "Y. Lao"
    },
    {
      "name": "Y. Zhang"
    },
    {
      "name": "Y. Zhu"
    },
    {
      "affs": [
        0
      ],
      "name": "S. Wu"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/0hjq8chtc2eam.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.21.753344",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753344v1.full",
  "id": "0hjq8chtc2eam",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753344v1",
  "language": null,
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1607|Advanced Proteomics Techniques and Applications"
    ]
  ],
  "openalex": "W7214443485",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753344v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-21",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/0hjq8chtc2eam.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:41Z",
      "native_id": "10.64898/2026.09.21.753344",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753344v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "PTMExplorer: A Multi-Dimensional Integrative Visualization Platform for Protein Post-Translational Modification Function and Structure",
  "title_text": "PTMExplorer: A Multi-Dimensional Integrative Visualization Platform for Protein Post-Translational Modification Function and Structure",
  "type": "preprint",
  "updated_at": "2026-10-30T12:24:41Z",
  "url": "https://research.draconitic.com/paper/0hjq8chtc2eam",
  "venue": "bioRxiv",
  "versions": []
}