{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T14:28:32Z","timestamp":1788532112220,"version":"build-2803163510"},"reference-count":33,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100007830","name":"Kitasato University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007830","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["21K06036"],"award-info":[{"award-number":["21K06036"]}],"id":[{"id":"10.13039\/501100001691","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>Proteomics provides a systematic and high-throughput approach to comprehensively characterize protein networks, enabling insights into cellular functions and disease mechanisms. Carbamidomethylation using iodoacetamide (IAA), a common method for cysteine alkylation, is known to cause nonspecific modifications that increase spectral complexity in mass spectrometry and reduce quantitative accuracy. Here, we established a reproducibility-focused 2-mercaptoethanol (2-ME)\/dimethyl sulfoxide (DMSO) workflow and systematically evaluated its quantitative performance at the proteome-wide level. Mouse liver proteomes were processed using either 2-ME\/DMSO or conventional IAA treatment, followed by liquid chromatography-tandem mass spectrometry (LC\u2013MS\/MS) analysis. The optimized 2-ME treatment increased the number of cysteine-modified peptides by 1.6- to 1.9-fold. Although total protein identifications were comparable, 77% of proteins exhibited improved sequence coverage with the optimized 2-ME treatment. Quantitative reproducibility was also enhanced, with the peptide quantified CV \u2264 20% increasing from 61.4% with IAA treatment to 86.1% with 2-ME treatment, and protein quantified CV \u2264 20% increasing from 80.6% with IAA treatment to 93.5% with 2-ME treatment. Application of this new workflow to ovarian clear cell carcinoma reliably detected cisplatin-induced alterations. The 2-ME\/DMSO workflow offers a simple and highly reproducible proteomics strategy for accurate quantitative proteomics.<\/jats:p>","DOI":"10.1021\/acs.jproteome.6c00010","type":"journal-article","created":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T06:43:47Z","timestamp":1778222627000},"page":"4524-4533","source":"Crossref","is-referenced-by-count":1,"title":["2-Mercaptoethanol\/DMSO\nWorkflow Enables Highly\nReproducible Quantitative Proteomics"],"prefix":"10.1021","volume":"25","author":[{"given":"Arisa","family":"Suto","sequence":"first","affiliation":[{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshihiro","family":"Ishikawa","sequence":"additional","affiliation":[{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toshihide","family":"Matsumoto","sequence":"additional","affiliation":[{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Makoto","family":"Itakura","sequence":"additional","affiliation":[{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]},{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshio","family":"Kodera","sequence":"additional","affiliation":[{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]},{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4496-2389","authenticated-orcid":true,"given":"Takashi","family":"Matsui","sequence":"additional","affiliation":[{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]},{"name":"Kitasato University , , 1-15-1 Kitasato, Minami-ku , , ,","place":["Sagamihara, Kanagawa, Japan, 252-0373"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,5,8]]},"reference":[{"key":"2026090409133930200_cit1","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/nature19949","article-title":"Mass-Spectrometric\nExploration of Proteome Structure and Function","volume":"537","author":"Aebersold","year":"2016","journal-title":"Nature"},{"key":"2026090409133930200_cit2","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1038\/s41586-025-08584-0","article-title":"Mass-Spectrometry-Based\nProteomics:\nFrom Single Cells to Clinical Applications","volume":"638","author":"Guo","year":"2025","journal-title":"Nature"},{"key":"2026090409133930200_cit3","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1021\/acsmeasuresciau.3c00068","article-title":"Comprehensive\nOverview of Bottom-Up Proteomics Using Mass Spectrometry","volume":"4","author":"Jiang","year":"2024","journal-title":"ACS Meas. Sci. Au"},{"key":"2026090409133930200_cit4","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1146\/annurev-biochem-061308-093216","article-title":"High-Resolution\nProteomics for Data-Driven Systems\nBiology","volume":"80","author":"Cox","year":"2011","journal-title":"Annu. Rev. Biochem."},{"issue":"9","key":"2026090409133930200_cit5","doi-asserted-by":"publisher","first-page":"3443","DOI":"10.1021\/acs.jproteome.7b00022","article-title":"The Impact of Commonly\nUsed Alkylating Agents on Artifactual\nPeptide Modification","volume":"16","author":"Hains","year":"2017","journal-title":"J. Proteome Res."},{"issue":"15","key":"2026090409133930200_cit6","doi-asserted-by":"publisher","first-page":"3576","DOI":"10.1021\/ac0103423","article-title":"Overalkylation of\na Protein Digest with Iodoacetamide","volume":"73","author":"Boja","year":"2001","journal-title":"Anal. Chem."},{"issue":"7","key":"2026090409133930200_cit7","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1074\/mcp.M116.064048","article-title":"Systematic Evaluation\nof Protein Reduction and Alkylation\nReveals Massive Unspecific Side Effects by Iodine-Containing Reagents","volume":"16","author":"Mu\u0308ller","year":"2017","journal-title":"Mol. Cell. Proteomics"},{"issue":"12","key":"2026090409133930200_cit8","doi-asserted-by":"publisher","first-page":"2574","DOI":"10.1039\/C7MB00393E","article-title":"Evaluation and Optimization\nof Reduction and Alkylation Methods to Maximize Peptide Identification\nwith MS-Based Proteomics","volume":"13","author":"Suttapitugsakul","year":"2017","journal-title":"Mol. Biosyst."},{"key":"2026090409133930200_cit9","doi-asserted-by":"publisher","first-page":"151485","DOI":"10.1016\/j.bbrc.2025.151485","article-title":"Reducing Offsite\nModifications Using\n2-Mercaptoethanol for LC-MS Analyses","volume":"753","author":"Suto","year":"2025","journal-title":"Biochem.\nBiophys. Res. Commun."},{"key":"2026090409133930200_cit10","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1107\/S2053230X2100203X","article-title":"Crystal Structure of\nHuman CRM1, Covalently Modified by 2-Mercaptoethanol on Cys528, in\nComplex with RanGTP","volume":"77","author":"Shaikhqasem","year":"2021","journal-title":"Acta Crystallogr. F Struct.\nBiol. Commun."},{"issue":"1","key":"2026090409133930200_cit11","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1006\/abio.1994.1016","article-title":"Analysis of Recombinant\nSchistosoma Mansoni Antigen\nRSmp28 by On-Line Liquid Chromatography-Mass Spectrometry Combined\nwith Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis","volume":"216","author":"Klarskov","year":"1994","journal-title":"Anal. Biochem."},{"issue":"6","key":"2026090409133930200_cit12","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1002\/jat.3948","article-title":"Oxidation\nof a Cysteine-Derived Nucleophilic Reagent by Dimethyl Sulfoxide in\nthe Amino Acid Derivative Reactivity Assay","volume":"40","author":"Akimoto","year":"2020","journal-title":"J. Appl. Toxicol."},{"issue":"48","key":"2026090409133930200_cit13","doi-asserted-by":"publisher","first-page":"25605","DOI":"10.1039\/c3ra45811c","article-title":"The Effect of DMSO in the Aqueous Thiol-Disulphide\nDynamic Covalent Chemistry of Model Pseudopeptides","volume":"3","author":"Atcher","year":"2013","journal-title":"RSC Adv."},{"issue":"5","key":"2026090409133930200_cit14","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1007\/s10812-013-9841-1","article-title":"Detection of Oxidation of L-Cysteine by Dimethyl Sulfoxide\nin Aqueous Solutions by IR Spectroscopy","volume":"80","author":"Papanyan","year":"2013","journal-title":"J.\nAppl. Spectrosc."},{"key":"2026090409133930200_cit15","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.bbrc.2021.02.041","article-title":"A Highly Efficient\nMethod for Extracting Peptides from a Single Mouse Hypothalamus","volume":"548","author":"Nakagawa","year":"2021","journal-title":"Biochem. Biophys. Res. Commun."},{"issue":"2","key":"2026090409133930200_cit16","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1021\/pr700658q","article-title":"Phase Transfer Surfactant-Aided\nTrypsin\nDigestion for Membrane Proteome Analysis","volume":"7","author":"Masuda","year":"2008","journal-title":"J.\nProteome Res."},{"key":"2026090409133930200_cit17","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/j.bbrc.2021.02.101","article-title":"Highly Accurate and\nPrecise Quantification\nStrategy Using Stable Isotope Dimethyl Labeling Coupled with GeLC-MS\/MS","volume":"550","author":"Konno","year":"2021","journal-title":"Biochem. Biophys. Res. Commun."},{"issue":"10","key":"2026090409133930200_cit18","doi-asserted-by":"publisher","first-page":"1837","DOI":"10.1016\/j.ajpath.2021.06.009","article-title":"Anaplastic Lymphoma\nKinase Overexpression Is Associated\nwith Aggressive Phenotypic Characteristics of Ovarian High-Grade Serous\nCarcinoma","volume":"191","author":"Matsumoto","year":"2021","journal-title":"Am. J. Pathol."},{"issue":"11","key":"2026090409133930200_cit19","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.3390\/biomedicines11113047","article-title":"CD39+CD55\u2013 Fb\nSubset Exhibits Myofibroblast-Like Phenotype and Is Associated with\nPain in Osteoarthritis of the Knee","volume":"11","author":"Tsuchiya","year":"2023","journal-title":"Biomedicines"},{"issue":"5","key":"2026090409133930200_cit20","doi-asserted-by":"publisher","first-page":"1564","DOI":"10.1021\/acs.jproteome.3c00146","article-title":"Development\nof a Simple and Stable NanoESI Spray System Using Suction Wind from\nthe MS Inlet","volume":"22","author":"Kawashima","year":"2023","journal-title":"J. Proteome Res."},{"issue":"5","key":"2026090409133930200_cit21","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger:\nUltrafast and Comprehensive Peptide Identification\nin Mass Spectrometry-Based Proteomics","volume":"14","author":"Kong","year":"2017","journal-title":"Nat.\nMethods"},{"issue":"1","key":"2026090409133930200_cit22","doi-asserted-by":"publisher","first-page":"3329","DOI":"10.1038\/s41467-025-58728-z","article-title":"MSFragger-DDA+\nEnhances Peptide Identification\nSensitivity with Full Isolation Window Search","volume":"16","author":"Yu","year":"2025","journal-title":"Nat. Commun."},{"issue":"9","key":"2026090409133930200_cit23","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1038\/s41592-020-0912-y","article-title":"Philosopher: A Versatile Toolkit\nfor Shotgun Proteomics Data Analysis","volume":"17","author":"da Veiga Leprevost","year":"2020","journal-title":"Nat. Methods"},{"key":"2026090409133930200_cit24","doi-asserted-by":"publisher","first-page":"100077","DOI":"10.1016\/j.mcpro.2021.100077","article-title":"IonQuant\nEnables Accurate and Sensitive\nLabel-Free Quantification with FDR-Controlled Match-between-Runs","volume":"20","author":"Yu","year":"2021","journal-title":"Mol. Cell. Proteomics"},{"issue":"1","key":"2026090409133930200_cit25","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","article-title":"Neural Networks and\nInterference Correction Enable Deep Proteome\nCoverage in High Throughput","volume":"17","author":"Demichev","year":"2020","journal-title":"Nat. Methods"},{"issue":"1","key":"2026090409133930200_cit26","doi-asserted-by":"publisher","first-page":"btac757","DOI":"10.1093\/bioinformatics\/btac757","article-title":"GSEApy: A\nComprehensive Package for Performing Gene\nSet Enrichment Analysis in Python","volume":"39","author":"Fang","year":"2023","journal-title":"Bioinformatics"},{"issue":"9","key":"2026090409133930200_cit27","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1093\/carcin\/bgab070","article-title":"Cytoplasmic EBP50 and Elevated PARP1\nAre Unfavorable Prognostic Factors in Ovarian Clear Cell Carcinoma","volume":"42","author":"Matsumoto","year":"2021","journal-title":"Carcinogenesis"},{"issue":"6550","key":"2026090409133930200_cit28","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1038\/377649a0","article-title":"Crystal Structure\nof Double-Stranded DNA Containing the Major Adduct of the Anticancer\nDrug Cisplatin","volume":"377","author":"Takahara","year":"1995","journal-title":"Nature"},{"issue":"24","key":"2026090409133930200_cit29","doi-asserted-by":"publisher","first-page":"10135","DOI":"10.1021\/ac1019792","article-title":"Alkylating Tryptic\nPeptides to Enhance Electrospray Ionization Mass Spectrometry Analysis","volume":"82","author":"Kulevich","year":"2010","journal-title":"Anal. Chem."},{"issue":"11","key":"2026090409133930200_cit30","doi-asserted-by":"publisher","first-page":"3989","DOI":"10.1021\/ac070558q","article-title":"Achieving Augmented Limits of Detection for Peptides\nwith Hydrophobic Alkyl Tags","volume":"79","author":"Frahm","year":"2007","journal-title":"Anal. Chem."},{"key":"2026090409133930200_cit31","doi-asserted-by":"publisher","DOI":"10.6061\/clinics\/2018\/e478s","article-title":"DNA Repair Pathways and Cisplatin\nResistance: An Intimate\nRelationship","volume":"73","author":"Rocha","year":"2018","journal-title":"Clinics. Universidade de Sao Paulo"},{"issue":"1","key":"2026090409133930200_cit32","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/s41596-018-0082-x","article-title":"Single-Pot,\nSolid-Phase-Enhanced Sample Preparation\nfor Proteomics Experiments","volume":"14","author":"Hughes","year":"2019","journal-title":"Nat. Protoc."},{"issue":"D1","key":"2026090409133930200_cit33","doi-asserted-by":"publisher","first-page":"D462","DOI":"10.1093\/nar\/gkae1032","article-title":"JPOST Environment Accelerates the\nReuse and Reanalysis of Public Proteome Mass Spectrometry Data","volume":"53","author":"Okuda","year":"2025","journal-title":"Nucleic Acids Res."}],"container-title":["Journal of Proteome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jproteome.6c00010","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/25\/9\/4524\/63219196\/acs.jproteome.6c00010.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/25\/9\/4524\/63219196\/acs.jproteome.6c00010.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T14:06:12Z","timestamp":1788530772000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jprobs\/article\/25\/9\/4524\/5075883\/2-Mercaptoethanol-DMSO-Workflow-Enables-Highly"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,8]]},"references-count":33,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,5,8]]},"published-print":{"date-parts":[[2026,9,4]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jproteome.6c00010","relation":{"has-preprint":[{"id-type":"doi","id":"10.64898\/2025.12.19.694883","asserted-by":"object"}]},"ISSN":["1535-3893","1535-3907"],"issn-type":[{"value":"1535-3893","type":"print"},{"value":"1535-3907","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,8]]}}}