{
  "abstract": "Protein-RNA interactions regulate nearly all levels of gene expression. Their characterization at the molecular basis is critical for understanding the function of protein-RNA complexes, both in cell homeostasis and pathology. Yet, molecular interactions underlying the formation of these complexes remain understudied. UV cross-linking mass spectrometry (XL-MS) is one of the leading approaches for in vitro identification of protein-RNA contact sites, and for providing structural information in the form of distance constraints crucial for the refinement of structural models. Our previously published CLIR-MS method enables qualitative characterization of protein-RNA interactions at residue-specific resolution but was not designed for highly accurate quantitative interpretation. Here, we present a XL-MS workflow based on irradiation with UV light that combines data-dependent acquisition (DDA) and parallel reaction monitoring (PRM) for simultaneous detection and characterization of protein-RNA interaction sites at residue-specific resolution, followed by label-free quantification of cross-linked products. We successfully apply our combined workflow to in vitro reconstituted protein-RNA complexes formed by the proteins TDP-43 and FOX1. We report on novel RNA interaction sites located in the oligomerization interface of the N-terminal domain (NTD) of TDP-43, and characterize quantitatively the process of RNA-induced monomerization of the NTD in an RNA titration experiment. We also investigate temperature-dependent differences in the efficiency of cross-link formation in the FOX1 complex. Our framework offers a unique and novel approach to comparative quantification of protein-RNA cross-links, overcoming the limitations imposed by conventional UV XL-MS methods.",
  "abstract_shown": true,
  "affiliations": [
    "ETH Zurich"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "name": "I. Smok"
    },
    {
      "name": "A. Zbinden"
    },
    {
      "name": "J. Osterroth"
    },
    {
      "name": "J. Jiang"
    },
    {
      "name": "F. H.- T. Allain"
    },
    {
      "name": "J. Hall"
    },
    {
      "name": "M. Polymenidou"
    },
    {
      "affs": [
        0
      ],
      "name": "A. Leitner"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8ryffc0282xys.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.15.756239",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.15.756239v1.full",
  "id": "8ryffc0282xys",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.15.756239v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "biophysics"
    ],
    [
      "openalex",
      "1607|Advanced Proteomics Techniques and Applications"
    ]
  ],
  "openalex": "W7223008554",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.15.756239v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-15",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/8ryffc0282xys.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:28:40Z",
      "native_id": "10.64898/2026.10.15.756239",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.15.756239v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:biophysics",
      "subfield": "biophysics"
    }
  ],
  "title": "A qualitative and quantitative framework for the characterization of protein-RNA interactions by cross-linking mass spectrometry (XL-MS)",
  "title_text": "A qualitative and quantitative framework for the characterization of protein-RNA interactions by cross-linking mass spectrometry (XL-MS)",
  "type": "preprint",
  "updated_at": "2026-10-30T12:28:40Z",
  "url": "https://research.draconitic.com/paper/8ryffc0282xys",
  "venue": "bioRxiv",
  "versions": []
}