{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T06:45:29Z","timestamp":1792133129667,"version":"4.4.0"},"reference-count":20,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB1565"],"award-info":[{"award-number":["SFB1565"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["469281184"],"award-info":[{"award-number":["469281184"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["P04"],"award-info":[{"award-number":["P04"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2026,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Protein\u2010nucleic acid (protein\u2010Nu) interactions are crucial for many cellular processes and biological functions. Crosslinking mass spectrometry (XL\u2010MS) has emerged as a powerful method for identifying these interactions. However, the analysis of protein\u2010Nu XL\u2010MS data requires an integrated workflow from raw data processing to results inspection and validation. Existing workflows for protein\u2010Nu XL\u2010MS often require switching between tools and considerable manual processing. Here, we introduce NuXLApp, an interactive web\u2010based application for data processing and results visualization in protein\u2010Nu XL\u2010MS studies. NuXLApp integrates the protein\u2010Nu crosslink search engine \u201cNuXL,\u201d machine\u2010learning models for peptide property prediction, and interactive result visualization within a reproducible workflow. It enables rapid validation of false discovery rate\u2010controlled crosslink spectrum match\u2010level identifications and facilitates collaboration and intuitive exploration of experimental results. In addition, NuXLApp generates a spectral library from identified protein\u2010Nu crosslinks to enable quantitative analysis of crosslinks using data\u2010independent acquisition (DIA). NuXLApp supports discovery\u2010driven identification of protein\u2010nucleic acid crosslinks and enables DIA\u2010based follow\u2010up experiments for their quantitative analysis. NuXLApp is open\u2010source and available via the OpenMS WebApps platform at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/nuxl.webapps.openms.de\/\">https:\/\/nuxl.webapps.openms.de\/<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1002\/pro.70820","type":"journal-article","created":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T05:58:28Z","timestamp":1792130308000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>NuXLApp<\/scp>\n                    : Interactive data analysis and visualization for protein\u2010nucleic acid crosslinking mass spectrometry"],"prefix":"10.1002","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-5748-0027","authenticated-orcid":false,"given":"Arslan","family":"Siraj","sequence":"first","affiliation":[{"name":"Applied Bioinformatics, Department of Computer Science University of T\u00fcbingen  T\u00fcbingen Germany"},{"name":"Institute for Bioinformatics and Medical Informatics University of T\u00fcbingen  T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1697-9201","authenticated-orcid":false,"given":"Sergei","family":"Moshkovskii","sequence":"additional","affiliation":[{"name":"Department of Clinical Chemistry University Medical Center G\u00f6ttingen  G\u00f6ttingen Germany"},{"name":"Research Group Bioanalytical Mass Spectrometry Max Planck Institute for Multidisciplinary Sciences  G\u00f6ttingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0118-9434","authenticated-orcid":false,"given":"Tom David","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Applied Bioinformatics, Department of Computer Science University of T\u00fcbingen  T\u00fcbingen Germany"},{"name":"Institute for Bioinformatics and Medical Informatics University of T\u00fcbingen  T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1837-5233","authenticated-orcid":false,"given":"Henning","family":"Urlaub","sequence":"additional","affiliation":[{"name":"Department of Clinical Chemistry University Medical Center G\u00f6ttingen  G\u00f6ttingen Germany"},{"name":"Research Group Bioanalytical Mass Spectrometry Max Planck Institute for Multidisciplinary Sciences  G\u00f6ttingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Kohlbacher","sequence":"additional","affiliation":[{"name":"Applied Bioinformatics, Department of Computer Science University of T\u00fcbingen  T\u00fcbingen Germany"},{"name":"Institute for Bioinformatics and Medical Informatics University of T\u00fcbingen  T\u00fcbingen Germany"},{"name":"Translational Bioinformatics University Hospital T\u00fcbingen  T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2833-6070","authenticated-orcid":false,"given":"Timo","family":"Sachsenberg","sequence":"additional","affiliation":[{"name":"Applied Bioinformatics, Department of Computer Science University of T\u00fcbingen  T\u00fcbingen Germany"},{"name":"Institute for Bioinformatics and Medical Informatics University of T\u00fcbingen  T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,15]]},"reference":[{"issue":"1","key":"e_1_2_8_2_1","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s13062-015-0096-z","article-title":"The progene hypothesis: the nucleoprotein world and how life began","volume":"10","author":"Altstein AD","year":"2015","journal-title":"Biol 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flexible method to improve labile PTM analysis in proteomics","volume":"22","author":"Polasky DA","year":"2023","journal-title":"Mol Cell Proteomics"},{"issue":"10","key":"e_1_2_8_13_1","doi-asserted-by":"crossref","first-page":"3368","DOI":"10.1021\/acs.jproteome.3c00341","article-title":"RNxQuest: an extension to the xQuest pipeline enabling analysis of protein\u2013RNA cross\u2010linking\/mass spectrometry data","volume":"22","author":"Sarnowski CP","year":"2023","journal-title":"J Proteome Res"},{"issue":"8","key":"e_1_2_8_14_1","doi-asserted-by":"crossref","DOI":"10.1002\/pmic.202300144","article-title":"Intensity and retention time prediction improves the rescoring of protein\u2010nucleic acid cross\u2010links","volume":"24","author":"Siraj A","year":"2024","journal-title":"Proteomics"},{"issue":"1","key":"e_1_2_8_15_1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.ceb.2009.01.003","article-title":"Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines","volume":"21","author":"Staley JP","year":"2009","journal-title":"Curr Opin Cell Biol"},{"issue":"7","key":"e_1_2_8_16_1","doi-asserted-by":"crossref","first-page":"3760","DOI":"10.1021\/pr900171m","article-title":"TOPPView: an open\u2010source viewer for mass spectrometry data","volume":"8","author":"Sturm M","year":"2009","journal-title":"J Proteome Res"},{"issue":"1","key":"e_1_2_8_17_1","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-19047-7","article-title":"Analysis of protein\u2010DNA interactions in chromatin by UV induced cross\u2010linking and mass spectrometry","volume":"11","author":"St\u00fctzer A","year":"2020","journal-title":"Nat Commun"},{"issue":"1","key":"e_1_2_8_18_1","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.cell.2018.11.004","article-title":"The human RNA\u2010binding proteome and its dynamics during translational arrest","volume":"176","author":"Trendel 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Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.70820","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/pro.70820","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.70820","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T05:58:30Z","timestamp":1792130310000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.70820"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,15]]},"references-count":20,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["10.1002\/pro.70820"],"URL":"https:\/\/doi.org\/10.1002\/pro.70820","archive":["Portico"],"relation":{},"ISSN":["0961-8368","1469-896X"],"issn-type":[{"value":"0961-8368","type":"print"},{"value":"1469-896X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,15]]},"assertion":[{"value":"2026-05-05","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication 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