{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:11:39Z","timestamp":1785420699782,"version":"3.56.0"},"reference-count":34,"publisher":"American Chemical Society (ACS)","issue":"28","license":[{"start":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T00:00:00Z","timestamp":1783641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006019","name":"Van Andel Institute","doi-asserted-by":"publisher","award":["SCR_027494"],"award-info":[{"award-number":["SCR_027494"]}],"id":[{"id":"10.13039\/100006019","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014559","name":"General Medical Council","doi-asserted-by":"publisher","award":["R35GM152184"],"award-info":[{"award-number":["R35GM152184"]}],"id":[{"id":"10.13039\/100014559","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,21]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Histone post-translational modifications (PTMs) are key regulators of chromatin architecture and gene expression. Although mass spectrometry (MS)-based data-independent acquisition (DIA) pipelines for histone PTM quantification are available, multiplexed targeted assays remain underdeveloped. Here, we present a derivatization-free parallel reaction monitoring (PRM) workflow for robust, quantitative, and site-specific analysis of major histone H3 and H4 PTMs. We employed highly efficient ArgC digestion to generate peptides of optimal length for liquid chromatography-tandem mass spectrometry (LC\u2013MS\/MS) while preserving endogenous PTMs, and we optimized chromatographic conditions to achieve isobaric separation and stable retention times. Co-eluting isobaric PTM species were confidently distinguished using site-specific fragment ions. The resulting PRM method enabled sensitive and reproducible detection of histone PTM isoforms across diverse biological systems. To illustrate its utility, we analyzed PTM dynamics in cells expressing histone H3.3 lysine-to-methionine substitutions and in cells treated with the histone deacetylase inhibitor entinostat, yielding results that correlated strongly with antibody-based readouts. This PRM platform provides a complementary, targeted approach to current chemical derivatization\u2013based methods, enabling reliable validation of selected histone PTMs.<\/jats:p>","DOI":"10.1021\/acsomega.6c02411","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T06:11:57Z","timestamp":1783663917000},"page":"42597-42609","source":"Crossref","is-referenced-by-count":0,"title":["A Derivatization-Free Parallel Reaction Monitoring-Based\nProteomics Workflow for Quantitative, Site-Specific Analysis of Histone\nPost-Translational Modifications"],"prefix":"10.1021","volume":"11","author":[{"given":"Hyoungjoo","family":"Lee","sequence":"first","affiliation":[{"name":"Van Andel Institute , , 333 Bostwick Ave NE , , ,","place":["Grand Rapids, Michigan, United States, 49503"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley K.","family":"Wiseman","sequence":"additional","affiliation":[{"name":"Van Andel Institute , , 333 Bostwick Ave NE , , ,","place":["Grand Rapids, Michigan, United States, 49503"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bailey M.","family":"Tibben","sequence":"additional","affiliation":[{"name":"Van Andel Institute , , 333 Bostwick Ave NE , , ,","place":["Grand Rapids, Michigan, United States, 49503"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ibukunoluwa","family":"Sodiya","sequence":"additional","affiliation":[{"name":"Van Andel Institute , , 333 Bostwick Ave NE , , ,","place":["Grand Rapids, Michigan, United States, 49503"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott B.","family":"Rothbart","sequence":"additional","affiliation":[{"name":"Van Andel Institute , , 333 Bostwick Ave NE , , ,","place":["Grand Rapids, Michigan, United States, 49503"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly T.","family":"Soper-Hopper","sequence":"additional","affiliation":[{"name":"Van Andel Institute , , 333 Bostwick Ave NE , , ,","place":["Grand Rapids, Michigan, United States, 49503"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1573-9719","authenticated-orcid":true,"given":"Ryan D.","family":"Sheldon","sequence":"additional","affiliation":[{"name":"Van Andel Institute , , 333 Bostwick Ave NE , , ,","place":["Grand Rapids, Michigan, United States, 49503"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,10]]},"reference":[{"issue":"9","key":"2026073009062938000_cit1","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/s41576-022-00468-7","article-title":"Histone post-translational\nmodifications - cause and consequence of genome function","volume":"23","author":"Milla\u0301n-Zambrano","year":"2022","journal-title":"Nat. Rev. Genet."},{"issue":"3","key":"2026073009062938000_cit2","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/cr.2011.22","article-title":"Regulation of chromatin by histone modifications","volume":"21","author":"Bannister","year":"2011","journal-title":"Cell Res."},{"key":"2026073009062938000_cit3","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/j.semcdb.2022.02.012","article-title":"Histone variant-specific post-translational modifications","volume":"135","author":"Joseph","year":"2023","journal-title":"Semin. Cell Dev. Biol."},{"issue":"10","key":"2026073009062938000_cit4","doi-asserted-by":"publisher","first-page":"798","DOI":"10.1038\/nmeth1100","article-title":"Mapping protein\npost-translational modifications with mass spectrometry","volume":"4","author":"Witze","year":"2007","journal-title":"Nat. Methods"},{"issue":"3","key":"2026073009062938000_cit5","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1042\/BCJ20200170","article-title":"Combinations of histone post-translational modifications","volume":"478","author":"Taylor","year":"2021","journal-title":"Biochem. J."},{"issue":"5","key":"2026073009062938000_cit6","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1111\/febs.15707","article-title":"Mass spectrometry-based characterization\nof histones in clinical samples: applications, progress, and challenges","volume":"289","author":"Noberini","year":"2022","journal-title":"FEBS J."},{"key":"2026073009062938000_cit7","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/bs.mie.2015.12.007","article-title":"Identification and Quantification\nof Histone PTMs Using High-Resolution Mass Spectrometry","volume":"574","author":"Karch","year":"2016","journal-title":"Methods Enzymol."},{"issue":"1","key":"2026073009062938000_cit8","doi-asserted-by":"publisher","first-page":"100897","DOI":"10.1016\/j.mcpro.2024.100897","article-title":"Development of a High-Throughput Platform for\nQuantitation of Histone Modifications on a New QTOF Instrument","volume":"24","author":"Zahn","year":"2025","journal-title":"Mol. Cell. Proteomics"},{"issue":"6","key":"2026073009062938000_cit9","doi-asserted-by":"publisher","first-page":"1696","DOI":"10.1074\/mcp.M114.046011","article-title":"EpiProfile Quantifies\nHistone Peptides With Modifications by Extracting Retention Time and\nIntensity in High-resolution Mass Spectra","volume":"14","author":"Yuan","year":"2015","journal-title":"Mol.\nCell. Proteomics"},{"key":"2026073009062938000_cit10","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/j.semcdb.2022.02.012","article-title":"Histone Variant-Specific Post-Translational Modifications","volume":"135","author":"Joseph","year":"2023","journal-title":"Semin. Cell Dev. Biol."},{"issue":"2","key":"2026073009062938000_cit11","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1038\/s41576-024-00759-1","article-title":"Multifunctional Histone Variants in Genome Function","volume":"26","author":"Wong","year":"2025","journal-title":"Nat. Rev. Genet."},{"issue":"5","key":"2026073009062938000_cit12","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1016\/j.cell.2010.08.011","article-title":"The Language of Histone Crosstalk","volume":"142","author":"Lee","year":"2010","journal-title":"Cell"},{"key":"2026073009062938000_cit13","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1007\/978-1-0716-1024-4_11","article-title":"Targeted Protein Quantification\nUsing Parallel Reaction Monitoring (PRM)","volume":"2228","author":"Barkovits","year":"2021","journal-title":"Methods\nMol. Biol."},{"issue":"1","key":"2026073009062938000_cit14","doi-asserted-by":"publisher","first-page":"4239","DOI":"10.1038\/s41467-024-48314-0","article-title":"Preserving ester-linked modifications reveals glutamate\nand aspartate mono-ADP-ribosylation by PARP1 and its reversal by PARG","volume":"15","author":"Longarini","year":"2024","journal-title":"Nat. Commun."},{"issue":"25","key":"2026073009062938000_cit15","doi-asserted-by":"publisher","first-page":"8704","DOI":"10.1021\/acs.analchem.1c00990","article-title":"Ultrasensitive\nNanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar\nArray LC Technology with Orbitrap Exploris 480 and FAIMS PRO","volume":"93","author":"Stejskal","year":"2021","journal-title":"Anal. Chem."},{"issue":"11","key":"2026073009062938000_cit16","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1016\/j.molmed.2019.09.003","article-title":"Dynamic Histone H3 Incorporation Fuels Metastatic Progression","volume":"25","author":"Simeonova","year":"2019","journal-title":"Trends Mol. Med."},{"key":"2026073009062938000_cit17","doi-asserted-by":"publisher","first-page":"12720","DOI":"10.1038\/srep12720","article-title":"Histone H4 acetylation required for chromatin decompaction\nduring DNA replication","volume":"5","author":"Ruan","year":"2015","journal-title":"Sci. Rep"},{"issue":"1","key":"2026073009062938000_cit18","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/s13072-020-00352-w","article-title":"Histone N-alpha terminal modifications:\ngenome regulation at the tip of the tail","volume":"13","author":"Demetriadou","year":"2020","journal-title":"Epigenetics\nChromatin"},{"issue":"7","key":"2026073009062938000_cit19","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document editor for creating\nand analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"issue":"2","key":"2026073009062938000_cit20","doi-asserted-by":"publisher","first-page":"17","DOI":"10.3390\/proteomes9020017","article-title":"Histone Sample\nPreparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed\nDecisions","volume":"9","author":"Daled","year":"2021","journal-title":"Proteomes"},{"issue":"16","key":"2026073009062938000_cit21","doi-asserted-by":"publisher","first-page":"9700","DOI":"10.1021\/acs.analchem.8b02448","article-title":"Lys-C\/Arg-C,\na More Specific and Efficient Digestion Approach for Proteomics Studies","volume":"90","author":"Wu","year":"2018","journal-title":"Anal. Chem."},{"issue":"7","key":"2026073009062938000_cit22","doi-asserted-by":"publisher","first-page":"100799","DOI":"10.1016\/j.mcpro.2024.100799","article-title":"Improved Mass Spectrometry-Based\nMethods Reveal Abundant Propionylation and Tissue-Specific Histone\nPropionylation Profiles","volume":"23","author":"Vai","year":"2024","journal-title":"Mol. Cell. Proteomics"},{"issue":"4","key":"2026073009062938000_cit23","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aax0021","article-title":"Deficient histone H3 propionylation by BRPF1-KAT6\ncomplexes in neurodevelopmental disorders and cancer","volume":"6","author":"Yan","year":"2020","journal-title":"Sci. Adv."},{"issue":"1","key":"2026073009062938000_cit24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/pmic.200300503","article-title":"Differentiation between peptides\ncontaining acetylated or tri-methylated lysines by mass spectrometry:\nan application for determining lysine 9 acetylation and methylation\nof histone H3","volume":"4","author":"Zhang","year":"2004","journal-title":"Proteomics"},{"issue":"10","key":"2026073009062938000_cit25","doi-asserted-by":"publisher","first-page":"7641","DOI":"10.1074\/jbc.M607900200","article-title":"Organismal differences in post-translational\nmodifications in histones H3 and H4","volume":"282","author":"Garcia","year":"2007","journal-title":"J. Biol.\nChem."},{"key":"2026073009062938000_cit26","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/978-1-61779-316-5_20","article-title":"Using ChIP-seq technology to generate\nhigh-resolution profiles of histone modifications","volume":"791","author":"O\u2019Geen","year":"2011","journal-title":"Methods Mol. Biol."},{"key":"2026073009062938000_cit27","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1007\/978-1-0716-4486-7_14","article-title":"Identification of Chromatin\nReaders Using a Peptide Pull-Down and Mass Spectrometry Integrated\nApproach","volume":"2919","author":"Stransky","year":"2025","journal-title":"Methods Mol. Biol."},{"issue":"1","key":"2026073009062938000_cit28","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1038\/s42003-021-01797-9","article-title":"Surfactant-assisted one-pot sample preparation for\nlabel-free single-cell proteomics","volume":"4","author":"Tsai","year":"2021","journal-title":"Commun. Biol."},{"issue":"6134","key":"2026073009062938000_cit29","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1126\/science.1232245","article-title":"Inhibition of PRC2 activity by a gain-of-function H3\nmutation found in pediatric glioblastoma","volume":"340","author":"Lewis","year":"2013","journal-title":"Science"},{"issue":"6765","key":"2026073009062938000_cit30","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/47412","article-title":"The Language of Covalent Histone Modifications","volume":"403","author":"Strahl","year":"2000","journal-title":"Nature"},{"issue":"8","key":"2026073009062938000_cit31","doi-asserted-by":"publisher","first-page":"4592","DOI":"10.1073\/pnas.96.8.4592","article-title":"A synthetic\ninhibitor of histone deacetylase, MS-27\u2013275, with marked in\nvivo antitumor activity against human tumors","volume":"96","author":"Saito","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"10","key":"2026073009062938000_cit32","doi-asserted-by":"publisher","first-page":"7983","DOI":"10.1074\/jbc.M110.194027","article-title":"H3K36 methylation\nantagonizes PRC2-mediated H3K27 methylation","volume":"286","author":"Yuan","year":"2011","journal-title":"J. Biol. Chem."},{"issue":"23","key":"2026073009062938000_cit33","doi-asserted-by":"publisher","first-page":"4876","DOI":"10.1016\/j.molcel.2021.10.008","article-title":"Histone H3.3 K27M and K36M mutations de-repress\ntransposable elements through perturbation of antagonistic chromatin\nmarks","volume":"81","author":"Chaouch","year":"2021","journal-title":"Mol. Cell"},{"issue":"3","key":"2026073009062938000_cit34","doi-asserted-by":"publisher","first-page":"247","DOI":"10.2217\/epi.11.23","article-title":"Antibody recognition of histone post-translational\nmodifications: emerging issues and future prospects","volume":"3","author":"Fuchs","year":"2011","journal-title":"Epigenomics"}],"container-title":["ACS Omega"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acsomega.6c02411","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/11\/28\/42597\/65848553\/acsomega.6c02411.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/11\/28\/42597\/65848553\/acsomega.6c02411.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:17:57Z","timestamp":1785417477000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acsodf\/article\/11\/28\/42597\/5205006\/A-Derivatization-Free-Parallel-Reaction-Monitoring"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,10]]},"references-count":34,"journal-issue":{"issue":"28","published-online":{"date-parts":[[2026,7,10]]},"published-print":{"date-parts":[[2026,7,21]]}},"URL":"https:\/\/doi.org\/10.1021\/acsomega.6c02411","relation":{},"ISSN":["2470-1343"],"issn-type":[{"value":"2470-1343","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,10]]}}}