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The roles of DNA R\/H HD modulator proteins are incompletely understood, in part, due to their relatively low cellular abundance and technical challenges in quantification. Here, we developed and validated targeted mass spectrometry assays quantifying DNA R\/H proteins, spanning functions in mismatch repair, Fanconi anemia, and transcriptional regulation, using complementary workflows for timsTOF and Orbitrap platforms. We built species-specific experiment spectral libraries that outperformed in silico libraries for target detection. Applying this pipeline to an HTT-Q140 knock-in mouse HD model, we observed that DNA R\/H protein abundances were largely unchanged in HD mice, while HTT and HAP40 showed increased nuclear association with disease progression. To facilitate translational research applications, we further developed a stable isotope dilution assay for absolute quantification of 11 human mismatch repair-associated proteins and generated an HTT knock-out human neuroblastoma cell line. Additionally, we used thermal proximity coaggregation profiling to characterize the endogenous interactomes of MMR proteins. We observed that HTT KO caused proteome down-regulation in selected DNA R\/H proteins and reshaped the MMR protein interactome, with the most pronounced changes observed for MLH1 and PMS1 interactions. Overall, we established a validated, transferable assay for quantifying DNA R\/H proteins in perturbation studies using human and mouse HD model systems and provide evidence that HTT influences the abundance and interaction landscape of proteins central to CAG repeat instability.<\/jats:p>","DOI":"10.64898\/2026.07.28.741339","type":"posted-content","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T19:05:11Z","timestamp":1785351911000},"source":"Crossref","is-referenced-by-count":0,"title":["Targeted quantification assays for DNA repair and handling proteins and interactions in Huntington\u2019s disease models"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5845-713X","authenticated-orcid":false,"given":"Todd M.","family":"Greco","sequence":"first","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5518-9651","authenticated-orcid":false,"given":"Josiah E.","family":"Hutton","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1884-8555","authenticated-orcid":false,"given":"Joshua L.","family":"Justice","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0945-5461","authenticated-orcid":false,"given":"Tavis J.","family":"Reed","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6041-0116","authenticated-orcid":false,"given":"Thomas F.","family":"Vogt","sequence":"additional","affiliation":[{"name":"CHDI Foundation, Princeton, NJ 08540"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9801-8951","authenticated-orcid":false,"given":"Brinda C.","family":"Prasad","sequence":"additional","affiliation":[{"name":"CHDI Foundation, Princeton, NJ 08540"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6533-2458","authenticated-orcid":false,"given":"Ileana M.","family":"Cristea","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026073113101669000_2026.07.28.741339v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2015.5"},{"key":"2026073113101669000_2026.07.28.741339v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.07.003"},{"key":"2026073113101669000_2026.07.28.741339v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.06.036"},{"key":"2026073113101669000_2026.07.28.741339v1.4","doi-asserted-by":"publisher","DOI":"10.7554\/ELIFE.64674"},{"key":"2026073113101669000_2026.07.28.741339v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-024-01653-6"},{"key":"2026073113101669000_2026.07.28.741339v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2023.12.009"},{"key":"2026073113101669000_2026.07.28.741339v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.11.038"},{"key":"2026073113101669000_2026.07.28.741339v1.8","doi-asserted-by":"publisher","DOI":"10.1177\/18796397251399751;SUBPAGE:STRING:FULL"},{"key":"2026073113101669000_2026.07.28.741339v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/S1474-4422(17)30161-8"},{"key":"2026073113101669000_2026.07.28.741339v1.10","doi-asserted-by":"crossref","first-page":"1426","DOI":"10.1038\/s41588-025-02191-5","article-title":"Genetic modifiers of somatic expansion and clinical phenotypes in Huntington\u2019s disease highlight shared and tissue-specific effects","volume":"57","year":"2025","journal-title":"Nat. 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