{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T18:21:18Z","timestamp":1790014878975,"version":"4.0.1"},"reference-count":43,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,1,10]],"date-time":"2023-01-10T00:00:00Z","timestamp":1673308800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100016714","name":"University of Sharjah","doi-asserted-by":"publisher","award":["2201110155"],"award-info":[{"award-number":["2201110155"]}],"id":[{"id":"10.13039\/100016714","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016714","name":"University of Sharjah","doi-asserted-by":"publisher","award":["2001110138"],"award-info":[{"award-number":["2001110138"]}],"id":[{"id":"10.13039\/100016714","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Untargeted multi-omics analysis of plasma is an emerging tool for the identification of novel biomarkers for evaluating disease prognosis, and for developing a better understanding of molecular mechanisms underlying human disease. The successful application of metabolomic and proteomic approaches relies on reproducibly quantifying a wide range of metabolites and proteins. Herein, we report the results of untargeted metabolomic and proteomic analyses from blood plasma samples following analyte extraction by two frequently-used solvent systems: chloroform\/methanol and methanol-only. Whole blood samples were collected from participants (n = 6) at University Hospital Sharjah (UHS) hospital, then plasma was separated and extracted by two methods: (i) methanol precipitation and (ii) 4:3 methanol:chloroform extraction. The coverage and reproducibility of the two methods were assessed by ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). The study revealed that metabolite extraction by methanol-only showed greater reproducibility for both metabolomic and proteomic quantifications than did methanol\/chloroform, while yielding similar peptide coverage. However, coverage of extracted metabolites was higher with the methanol\/chloroform precipitation.<\/jats:p>","DOI":"10.3390\/ijms24021354","type":"journal-article","created":{"date-parts":[[2023,1,11]],"date-time":"2023-01-11T02:06:03Z","timestamp":1673402763000},"page":"1354","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0371-7440","authenticated-orcid":false,"given":"Ruba A.","family":"Zenati","sequence":"first","affiliation":[{"name":"Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander D.","family":"Giddey","sequence":"additional","affiliation":[{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5621-9851","authenticated-orcid":false,"given":"Hamza M.","family":"Al-Hroub","sequence":"additional","affiliation":[{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yousra A.","family":"Hagyousif","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1580-2589","authenticated-orcid":false,"given":"Waseem","family":"El-Huneidi","sequence":"additional","affiliation":[{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1315-0609","authenticated-orcid":false,"given":"Yasser","family":"Bustanji","sequence":"additional","affiliation":[{"name":"Department of Basic and Clinical Pharmacology, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"School of Pharmacy, The University of Jordan, Amman 11942, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5972-0681","authenticated-orcid":false,"given":"Eman","family":"Abu-Gharbieh","sequence":"additional","affiliation":[{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7210-7964","authenticated-orcid":false,"given":"Mohammad A. Y.","family":"Alqudah","sequence":"additional","affiliation":[{"name":"Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohd","family":"Shara","sequence":"additional","affiliation":[{"name":"Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4182-065X","authenticated-orcid":false,"given":"Ahmad Y.","family":"Abuhelwa","sequence":"additional","affiliation":[{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2331-8532","authenticated-orcid":false,"given":"Nelson C.","family":"Soares","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0169-7538","authenticated-orcid":false,"given":"Mohammad H.","family":"Semreen","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates"},{"name":"Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1016\/j.csbj.2021.01.009","article-title":"Multi-omics approaches in cancer research with applications in tumor subtyping, prognosis, and diagnosis","volume":"19","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1038\/s41596-022-00710-w","article-title":"Using MetaboAnalyst 5.0 for LC\u2013HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data","volume":"17","author":"Pang","year":"2022","journal-title":"Nat. Protoc."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"bbab454","DOI":"10.1093\/bib\/bbab454","article-title":"A roadmap for multi-omics data integration using deep learning","volume":"23","author":"Kang","year":"2021","journal-title":"Briefings Bioinform."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"W527","DOI":"10.1093\/nar\/gkac376","article-title":"OmicsNet 2.0: A web-based platform for multi-omics integration and network visual analytics","volume":"50","author":"Zhou","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"eabo6764","DOI":"10.1126\/sciadv.abo6764","article-title":"Unified epigenomic, transcriptomic, proteomic, and metabolomic taxonomy of Alzheimer\u2019s disease progression and heterogeneity","volume":"8","author":"Adewale","year":"2022","journal-title":"Sci. Adv."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"828382","DOI":"10.3389\/fnins.2022.828382","article-title":"Integrated Metabolomics and Proteomics Analysis of Urine in a Mouse Model of Posttraumatic Stress Disorder","volume":"16","author":"Zhou","year":"2022","journal-title":"Front. Neurosci."},{"key":"ref_7","first-page":"130656","article-title":"Integrating proteomics and metabolomics approaches to elucidate the ripening process in white Psidium guajava","volume":"367","author":"Aluja","year":"2021","journal-title":"Food Chem."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"104581","DOI":"10.1016\/j.jprot.2022.104581","article-title":"Integrating serum proteomics and metabolomics to compare the common and distinct features between acute aggressive ischemic stroke (APIS) and acute non-aggressive ischemic stroke (ANPIS)","volume":"261","author":"Lai","year":"2022","journal-title":"J. Proteom."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1039\/D1AY00060H","article-title":"Simultaneous metabolomics and proteomics analysis of plasma-derived extracellular vesicles","volume":"13","author":"Guan","year":"2021","journal-title":"Anal. Methods"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"756847","DOI":"10.3389\/fgene.2021.756847","article-title":"Omics Technologies Toward Systems Biology","volume":"12","author":"Maghuly","year":"2021","journal-title":"Front. Genet."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"D\u00edaz-Beltr\u00e1n, L., Gonz\u00e1lez-Olmedo, C., Luque-Caro, N., D\u00edaz, C., Mart\u00edn-Bl\u00e1zquez, A., Fern\u00e1ndez-Navarro, M., Ortega-Granados, A., G\u00e1lvez-Montosa, F., Vicente, F., and del Palacio, J.P. (2021). Human Plasma Metabolomics for Biomarker Discovery: Targeting the Molecular Subtypes in Breast Cancer. Cancers, 13.","DOI":"10.3390\/cancers13010147"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"100474","DOI":"10.1016\/j.scp.2021.100474","article-title":"NMR spectroscopy as a \u201cgreen analytical method\u201d in metabolomics and proteomics studies","volume":"22","author":"Mielko","year":"2021","journal-title":"Sustain. Chem. Pharm."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"P30","DOI":"10.1089\/gen.41.P1.10","article-title":"Advances in Omics Protocols","volume":"41","author":"Sarkar","year":"2021","journal-title":"Genet. Eng. Biotechnol. News"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Martias, C., Baroukh, N., Mavel, S., Blasco, H., Lef\u00e8vre, A., Roch, L., Montigny, F., Gatien, J., Schibler, L., and Dufour-Rainfray, D. (2021). Optimization of Sample Preparation for Metabolomics Exploration of Urine, Feces, Blood and Saliva in Humans Using Combined NMR and UHPLC-HRMS Platforms. Molecules, 26.","DOI":"10.3390\/molecules26144111"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1007\/s11745-001-0843-0","article-title":"Comparison of the bligh and dyer and folch methods for total lipid determination in a broad range of marine tissue","volume":"36","author":"Iverson","year":"2001","journal-title":"Lipids"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1194\/jlr.D023036","article-title":"The BUME method: A novel automated chloroform-free 96-well total lipid extraction method for blood plasma [S]","volume":"53","author":"Forsberg","year":"2012","journal-title":"J. Lipid Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/s11745-013-3760-z","article-title":"An Improved High-Throughput Lipid Extraction Method for the Analysis of Human Brain Lipids","volume":"48","author":"Abbott","year":"2013","journal-title":"Lipids"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"5766","DOI":"10.1021\/ac500317c","article-title":"Objective Set of Criteria for Optimization of Sample Preparation Procedures for Ultra-High Throughput Untargeted Blood Plasma Lipid Profiling by Ultra Performance Liquid Chromatography\u2013Mass Spectrometry","volume":"86","author":"Sarafian","year":"2014","journal-title":"Anal. Chem."},{"key":"ref_19","first-page":"911","article-title":"A rapid method of total lipid extraction and purification","volume":"37","author":"Bligh","year":"1959","journal-title":"J. Lipid Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3074","DOI":"10.1194\/jlr.D008532","article-title":"Blood sphingolipidomics in healthy humans: Impact of sample collection methodology","volume":"51","author":"Hammad","year":"2010","journal-title":"J. Lipid Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.4155\/bio.11.122","article-title":"Sample preparation prior to the LC\u2013MS-based metabolomics\/metabonomics of blood-derived samples","volume":"3","author":"Gika","year":"2011","journal-title":"Bioanalysis"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"5433","DOI":"10.1021\/ac5005103","article-title":"Quantitating metabolites in protein precipitated serum using NMR spectroscopy","volume":"86","author":"Gowda","year":"2014","journal-title":"Anal. Chem."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"339983","DOI":"10.1016\/j.aca.2022.339983","article-title":"Analytical strategies to profile the internal chemical exposome and the metabolome of human placenta","volume":"1219","author":"Monfort","year":"2022","journal-title":"Anal. Chim. Acta"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Alsoud, L.O., Soares, N.C., Al-Hroub, H.M., Mousa, M., Kasabri, V., Bulatova, N., Suyagh, M., Alzoubi, K.H., El-Huneidi, W., and Abu-Irmaileh, B. (2022). Identification of Insulin Resistance Biomarkers in Metabolic Syndrome Detected by UHPLC-ESI-QTOF-MS. Metab., 12.","DOI":"10.3390\/metabo12060508"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Kiseleva, O., Kurbatov, I., Ilgisonis, E., and Poverennaya, E. (2021). Defining Blood Plasma and Serum Metabolome by GC-MS. Metabolites, 12.","DOI":"10.3390\/metabo12010015"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"981","DOI":"10.4155\/bio-2015-0010","article-title":"Methods used to increase the comprehensive coverage of urinary and plasma metabolomes by MS","volume":"8","author":"Chen","year":"2016","journal-title":"Bioanalysis"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1074\/mcp.M115.053702","article-title":"Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology","volume":"15","author":"Coman","year":"2016","journal-title":"Mol. Cell. Proteom."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1007\/s00280-022-04478-4","article-title":"Mass spectroscopy-based proteomics and metabolomics analysis of triple-positive breast cancer cells treated with tamoxifen and\/or trastuzumab","volume":"90","author":"Sharaf","year":"2022","journal-title":"Cancer Chemother. Pharmacol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1002\/pmic.200200500","article-title":"Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks","volume":"4","author":"Weckwerth","year":"2004","journal-title":"Proteomics."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1038\/nprot.2016.136","article-title":"The MaxQuant computational platform for mass spectrometry-based shotgun proteomics","volume":"11","author":"Tyanova","year":"2016","journal-title":"Nat. Protoc."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"86","DOI":"10.2174\/138920209787847050","article-title":"High-Throughput Omics Technologies: Potential Tools for the Investigation of Influences of EMF on Biological Systems","volume":"10","author":"Blankenburg","year":"2009","journal-title":"Curr. Genom."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1194\/jlr.D700041-JLR200","article-title":"Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics* s\u20de","volume":"49","author":"Matyash","year":"2008","journal-title":"J. Lipid Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/S0021-9258(18)64849-5","article-title":"A simple method for the isolation and purification of total lipides from animal tissues","volume":"226","author":"Folch","year":"1957","journal-title":"J. Biol. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"496","DOI":"10.3390\/metabo2030496","article-title":"Separation Technique for the Determination of Highly Polar Metabolites in Biological Samples","volume":"2","author":"Iwasaki","year":"2012","journal-title":"Metabolites"},{"key":"ref_35","unstructured":"Chou, S., and Spoo, W. (1997). Toxicological Profile for Chloroform, US Department of Health and Human Services."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Sekar, A., Varghese, G.K., and Varma, M. (2022). Chloroform\u2014An Emerging Pollutant in the Air. New Trends in Emerging Environmental Contaminants, Springer.","DOI":"10.1007\/978-981-16-8367-1_6"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"879","DOI":"10.3389\/fneur.2019.00879","article-title":"Comparison of Single Phase and Biphasic Extraction Protocols for Lipidomic Studies Using Human Plasma","volume":"10","author":"Wong","year":"2019","journal-title":"Front. Neurol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"389","DOI":"10.3390\/metabo5020389","article-title":"An Efficient Single Phase Method for the Extraction of Plasma Lipids","volume":"5","author":"Alshehry","year":"2015","journal-title":"Metabolites"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"5859","DOI":"10.1007\/s00216-018-1200-x","article-title":"One- vs two-phase extraction: Re-evaluation of sample preparation procedures for untargeted lipidomics in plasma samples","volume":"410","author":"Gil","year":"2018","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"6511","DOI":"10.1039\/D0AN01319F","article-title":"Assessment of human plasma and urine sample preparation for reproducible and high-throughput UHPLC-MS clinical metabolic phenotyping","volume":"145","author":"Southam","year":"2020","journal-title":"Analyst"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1039\/C8AN01574K","article-title":"New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells","volume":"144","author":"Couvillion","year":"2019","journal-title":"Analyst"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2513","DOI":"10.1074\/mcp.M113.031591","article-title":"Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ","volume":"13","author":"Cox","year":"2014","journal-title":"Mol. Cell. Proteom."},{"key":"ref_43","first-page":"559","article-title":"Quantitation of microgram amounts of protein in SDS-mercaptoethanol-tris electrophoresis sample buffer","volume":"6","author":"Ramagli","year":"1985","journal-title":"Anal. Biochem."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/2\/1354\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:05:44Z","timestamp":1760119544000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/2\/1354"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,10]]},"references-count":43,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2023,1]]}},"alternative-id":["ijms24021354"],"URL":"https:\/\/doi.org\/10.3390\/ijms24021354","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,10]]}}}