{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T11:43:48Z","timestamp":1793447028008,"version":"4.5.0"},"reference-count":34,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000165","name":"Division of Chemistry","doi-asserted-by":"publisher","award":["2305182"],"award-info":[{"award-number":["2305182"]}],"id":[{"id":"10.13039\/100000165","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P30CA225520"],"award-info":[{"award-number":["P30CA225520"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015582","name":"Ovarian Cancer Academy","doi-asserted-by":"publisher","award":["HT94252310175"],"award-info":[{"award-number":["HT94252310175"]}],"id":[{"id":"10.13039\/100015582","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI177469"],"award-info":[{"award-number":["R01AI177469"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000005","name":"U.S. Department of Defense","doi-asserted-by":"publisher","award":["OC220161"],"award-info":[{"award-number":["OC220161"]}],"id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Ascites from ovarian cancer patients are increasingly recognized as a valuable biofluid for cancer research, as its protein composition reflects the disease state and may reveal biomarkers of treatment sensitivity and response. However, the detection of low-abundance proteins is hindered by the presence of highly abundant proteins such as albumin. In this study, we evaluated five protein preparation methods for their effectiveness in depleting high-abundance or enriching low-abundance proteins in ovarian cancer ascites. The Norgen (Nor), Minutes (Min), and Perchloric acid (PerCA) methods were based on abundant protein depletion, while the Urine (Uri) and Nanomics (Nano) kits focused on low-abundance protein enrichment. Processed samples were analyzed using label-free quantitative bottom-up proteomics by LC-MS\/MS, followed by a bioinformatics assessment. Compared with undepleted ascites (UnD), Min, Nor, Nano, and PerCA increased protein identifications, whereas Uri produced profiles similar to those of UnD. Notably, PerCA and Nano enabled the identification of distinct protein subsets associated with cancer-related pathways, including immune responses and autophagy. PerCA enriched transmembrane and secreted immunomodulatory glycoproteins, whereas Nano enrichment primarily captured secreted, nuclear, and cytoplasmic soluble proteins. Overall, our results show that both high-abundance protein depletion and low-abundance enrichment improve ascites proteome coverage, each offering distinct advantages in identifying biologically relevant low-abundance proteins.<\/jats:p>","DOI":"10.1021\/acs.jproteome.6c00382","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T15:01:38Z","timestamp":1787151698000},"page":"5011-5021","source":"Crossref","is-referenced-by-count":1,"title":["Targeted Modulation\nof Abundant Proteins Enhances\nProteomic Profiling of Ovarian Cancer Ascites: A Pilot Technical Workflow\nComparison"],"prefix":"10.1021","volume":"25","author":[{"given":"Zongkai","family":"Peng","sequence":"first","affiliation":[{"name":"The University of Oklahoma , , , ,","place":["Norman, Oklahoma, United States, 73019"]},{"name":"University of Oklahoma Health Campus , , , ,","place":["Oklahoma City, Oklahoma, United States, 73104"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Lausen","sequence":"additional","affiliation":[{"name":"University of Oklahoma Health Campus , , , ,","place":["Oklahoma City, Oklahoma, United States, 73104"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7606-8245","authenticated-orcid":true,"given":"Doris M.","family":"Benbrook","sequence":"additional","affiliation":[{"name":"University of Oklahoma Health Campus , , , ,","place":["Oklahoma City, Oklahoma, United States, 73104"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0370-7450","authenticated-orcid":true,"given":"Zhibo","family":"Yang","sequence":"additional","affiliation":[{"name":"The University of Oklahoma , , , ,","place":["Norman, Oklahoma, United States, 73019"]},{"name":"University of Oklahoma Health Campus , , , ,","place":["Oklahoma City, Oklahoma, United States, 73104"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6813-7527","authenticated-orcid":true,"given":"Nagib","family":"Ahsan","sequence":"additional","affiliation":[{"name":"The University of Oklahoma , , , ,","place":["Norman, Oklahoma, United States, 73019"]},{"name":"University of Oklahoma , , , ,","place":["Norman, Oklahoma, United States, 73019"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,19]]},"reference":[{"issue":"1","key":"2026090409131045800_cit1","doi-asserted-by":"publisher","first-page":"10","DOI":"10.3322\/caac.21871","article-title":"Cancer statistics,\n2025","volume":"75","author":"Siegel","year":"2025","journal-title":"Cancer J. Clin."},{"issue":"12","key":"2026090409131045800_cit2","doi-asserted-by":"publisher","first-page":"2885","DOI":"10.3390\/cancers14122885","article-title":"Current and emerging\nmethods for ovarian cancer screening\nand diagnostics: a comprehensive review","volume":"14","author":"Liberto","year":"2022","journal-title":"Cancers"},{"issue":"1","key":"2026090409131045800_cit3","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/s41416-020-0875-x","article-title":"The untapped potential\nof ascites in ovarian cancer research and treatment","volume":"123","author":"Ford","year":"2020","journal-title":"Br. J. Cancer."},{"issue":"1","key":"2026090409131045800_cit4","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s12943-025-02438-z","article-title":"Harnessing\novarian cancer ascites for translational\nscience: models, biomarkers, and therapeutics","volume":"24","author":"Dogra","year":"2025","journal-title":"Mol. Cancer"},{"issue":"4","key":"2026090409131045800_cit5","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1038\/nrc3432","article-title":"Meeting\nthe challenge of ascites\nin ovarian cancer: new avenues for therapy and research","volume":"13","author":"Kipps","year":"2013","journal-title":"Nat. Rev. Cancer"},{"key":"2026090409131045800_cit6","doi-asserted-by":"publisher","first-page":"256","DOI":"10.3389\/fonc.2013.00256","article-title":"Getting to know\novarian cancer ascites: opportunities\nfor targeted therapy-based translational research","volume":"3","author":"Ahmed","year":"2013","journal-title":"Front. Oncol."},{"key":"2026090409131045800_cit7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10147-012-0396-6","article-title":"Malignant ascites:\npathophysiology and treatment","volume":"18","author":"Cavazzoni","year":"2013","journal-title":"Int. J. Clin.\nOncol."},{"key":"2026090409131045800_cit8","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1021\/acs.jproteome.5c00771","article-title":"Toward Proteomic-Based Prediction of Ex Vivo Platinum\nSensitivity in Ovarian Cancer Ascitic Cellular Aggregates: A Pilot\nStudy","volume":"25","author":"Scanlan","year":"2026","journal-title":"J. Proteome Res."},{"issue":"3","key":"2026090409131045800_cit9","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1007\/s12079-022-00698-8","article-title":"Friend and\nfoe: the regulation network\nof ascites components in ovarian cancer progression","volume":"17","author":"Geng","year":"2023","journal-title":"J. Cell Commun. Signaling"},{"key":"2026090409131045800_cit10","doi-asserted-by":"publisher","first-page":"2074","DOI":"10.3390\/biomedicines13092074","article-title":"Increased\nIGF2 and Immunosuppressive\nCell Populations in Ascites of Patients with Recurrent High-Grade\nSerous Ovarian Cancer","volume":"13","author":"Mortan","year":"2025","journal-title":"Biomedicines"},{"key":"2026090409131045800_cit11","doi-asserted-by":"publisher","first-page":"27","DOI":"10.36255\/exon-publications-ovarian-cancer-malignant-ascites","volume-title":"Chemoresistance\nin ovarian\ncancer: The role of Malignant ascites","author":"Nunes","year":"2022"},{"key":"2026090409131045800_cit12","doi-asserted-by":"publisher","first-page":"101755","DOI":"10.1016\/j.bbrep.2024.101755","article-title":"Ovarian cancer ascites proteomic\nprofile reflects metabolic changes during disease progression","volume":"39","author":"Almeida-Nunes","year":"2024","journal-title":"Biochem. Biophys. 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Biochem."},{"issue":"6","key":"2026090409131045800_cit14","doi-asserted-by":"publisher","first-page":"2895","DOI":"10.21873\/anticanres.15071","article-title":"Proteomic analysis\nof malignant ascites\nfrom patients with pancreatic ductal adenocarcinoma","volume":"41","author":"Kitamura","year":"2021","journal-title":"Anticancer Res."},{"issue":"12","key":"2026090409131045800_cit15","doi-asserted-by":"publisher","first-page":"3558","DOI":"10.1074\/mcp.M114.041194","article-title":"Proteome-metabolome\nprofiling of ovarian cancer ascites reveals novel components involved\nin intercellular communication","volume":"13","author":"Shender","year":"2014","journal-title":"Mol. Cell. Proteomics"},{"issue":"20","key":"2026090409131045800_cit16","doi-asserted-by":"publisher","first-page":"2300150","DOI":"10.1002\/pmic.202300150","article-title":"Proteomics\nevaluation of five economical commercial abundant protein depletion\nkits for enrichment of diseases-specific biomarkers from blood serum","volume":"23","author":"Ahsan","year":"2023","journal-title":"Proteomics"},{"issue":"1","key":"2026090409131045800_cit17","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.pcl.2012.10.002","article-title":"Human milk composition:\nnutrients and bioactive factors","volume":"60","author":"Ballard","year":"2013","journal-title":"Pediatr. Clin."},{"issue":"8","key":"2026090409131045800_cit18","doi-asserted-by":"publisher","first-page":"2670","DOI":"10.3390\/nu13082670","article-title":"Osteopontin\nlevels in human milk are related to maternal nutrition and infant\nhealth and growth","volume":"13","author":"Aksan","year":"2021","journal-title":"Nutrients"},{"issue":"37","key":"2026090409131045800_cit19","doi-asserted-by":"publisher","first-page":"42507","DOI":"10.1021\/acsomega.5c03776","article-title":"Enrichment\nof Low-Abundance\nand Low-Molecular-Weight Proteins in Human Milk Using Mass Spectrometry-Based\nProteomics","volume":"10","author":"Singh","year":"2025","journal-title":"ACS Omega"},{"key":"2026090409131045800_cit20","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1016\/j.jprot.2015.05.010","article-title":"Is isolation\nof comprehensive human\nplasma peptidomes an achievable quest?","volume":"127","author":"Mahboob","year":"2015","journal-title":"J. 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Adv."},{"issue":"4","key":"2026090409131045800_cit27","doi-asserted-by":"publisher","first-page":"888","DOI":"10.3390\/nano11040888","article-title":"Hard and Soft\nProtein Corona of Nanomaterials: Analysis\nand Relevance","volume":"11","author":"Garci\u0301a-A\u0301lvarez","year":"2021","journal-title":"Nanomaterials"},{"key":"2026090409131045800_cit28","doi-asserted-by":"publisher","first-page":"172273","DOI":"10.1016\/j.scitotenv.2024.172273","article-title":"Urine proteome\nprofile of firefighters\nwith exposure to emergency fire-induced smoke: A pilot study to identify\npotential carcinogenic effects","volume":"927","author":"Hwang","year":"2024","journal-title":"Sci. Total Environ."},{"issue":"2","key":"2026090409131045800_cit29","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1021\/acs.analchem.2c03299","article-title":"Cancer\nserum atlas-supported precise pan-targeted proteomics\nenable multicancer detection","volume":"95","author":"Hu","year":"2023","journal-title":"Anal. Chem."},{"issue":"3","key":"2026090409131045800_cit30","doi-asserted-by":"publisher","first-page":"267","DOI":"10.3390\/cells15030267","article-title":"Identification and Experimental Validation\nof Triosephosphate Isomerase 1 as a Functional Biomarker of SHetA2\nSensitivity in Ovarian Cancer","volume":"15","author":"Mortan","year":"2026","journal-title":"Cells"},{"issue":"5","key":"2026090409131045800_cit31","doi-asserted-by":"publisher","first-page":"2286","DOI":"10.1021\/pr1011087","article-title":"In-depth proteomics\nof ovarian cancer ascites: combining shotgun proteomics and selected\nreaction monitoring mass spectrometry","volume":"10","author":"Elschenbroich","year":"2011","journal-title":"J. Proteome\nRes."},{"issue":"3","key":"2026090409131045800_cit32","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1021\/pr900729g","article-title":"Combinatorial peptide libraries facilitate development\nof multiple reaction monitoring assays for low-abundance proteins","volume":"9","author":"Drabovich","year":"2010","journal-title":"J. Proteome Res."},{"key":"2026090409131045800_cit33","doi-asserted-by":"publisher","first-page":"2723","DOI":"10.1021\/acs.jproteome.5c01056","article-title":"Systematic Evaluation\nof Depletion and Enrichment Technologies for Platelet-Free Plasma\nProteomics","volume":"25","author":"Al Siblani","year":"2026","journal-title":"J. Proteome Res."},{"issue":"4","key":"2026090409131045800_cit34","doi-asserted-by":"publisher","first-page":"925","DOI":"10.1021\/pr050415p","article-title":"Beyond linker histones\nand high mobility group proteins:\nglobal profiling of perchloric acid soluble proteins","volume":"5","author":"Zougman","year":"2006","journal-title":"J. Proteome Res."}],"container-title":["Journal of Proteome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jproteome.6c00382","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/25\/9\/5011\/66879143\/acs.jproteome.6c00382.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/25\/9\/5011\/66879143\/acs.jproteome.6c00382.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T14:05:13Z","timestamp":1788530713000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jprobs\/article\/25\/9\/5011\/5276668\/Targeted-Modulation-of-Abundant-Proteins-Enhances"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,19]]},"references-count":34,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,8,19]]},"published-print":{"date-parts":[[2026,9,4]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jproteome.6c00382","relation":{},"ISSN":["1535-3893","1535-3907"],"issn-type":[{"value":"1535-3893","type":"print"},{"value":"1535-3907","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,19]]}}}