{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T12:00:33Z","timestamp":1784721633496,"version":"3.55.0"},"reference-count":38,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,5,30]],"date-time":"2022-05-30T00:00:00Z","timestamp":1653868800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81720108032 81930109"],"award-info":[{"award-number":["81720108032 81930109"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFA1301300"],"award-info":[{"award-number":["2021YFA1301300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Pharmacol."],"abstract":"<jats:p>Discovery of disease biomarker based on untargeted metabolomics is informative for pathological mechanism studies and facilitates disease early diagnosis. Numerous of metabolomic strategies emerge due to different sample properties or experimental purposes, thus, methodological evaluation before sample analysis is essential and necessary. In this study, sample preparation, data processing procedure and metabolite identification strategy were assessed aiming at the discovery of biomarker of breast cancer. First, metabolite extraction by different solvents, as well as the necessity of vacuum-dried and re-dissolution, was investigated. The extraction efficiency was assessed based on the number of eligible components (components with MS\/MS data acquired), which was more reasonable for metabolite identification. In addition, a simplified data processing procedure was proposed involving the OPLS-DA, primary screening for eligible components, and secondary screening with constraints including VIP, fold change and <jats:italic>p<\/jats:italic> value. Such procedure ensured that only differential candidates were subjected to data interpretation, which greatly reduced the data volume for database search and improved analysis efficiency. Furthermore, metabolite identification and annotation confidence were enhanced by comprehensive consideration of mass and MS\/MS errors, isotope similarity, fragmentation match, and biological source confirmation. On this basis, the optimized strategy was applied for the analysis of serum samples of breast cancer, according to which the discovery of differential metabolites highly encouraged the independent biomarkers\/indicators used for disease diagnosis and chemotherapy evaluation clinically. Therefore, the optimized strategy simplified the process of differential metabolite exploration, which laid a foundation for biomarker discovery and studies of disease mechanism.<\/jats:p>","DOI":"10.3389\/fphar.2022.894099","type":"journal-article","created":{"date-parts":[[2022,5,30]],"date-time":"2022-05-30T06:45:11Z","timestamp":1653893111000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Evaluation of Untargeted Metabolomic Strategy for the Discovery of Biomarker of Breast Cancer"],"prefix":"10.3389","volume":"13","author":[{"given":"Xujun","family":"Ruan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lirong","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiuling","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiping","family":"Hao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dandan","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,5,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"23","DOI":"10.3389\/fbioe.2015.00023","article-title":"Analytical Methods in Untargeted Metabolomics: State of the Art in 2015","volume":"3","author":"Alonso","year":"2015","journal-title":"Front. Bioeng. Biotechnol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"11321","DOI":"10.1021\/acs.analchem.1c02673","article-title":"Integration of Chemical Derivatization and In-Source Fragmentation Mass Spectrometry for High-Coverage Profiling of Submetabolomes","volume":"93","author":"An","year":"2021","journal-title":"Anal. Chem."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s11306-016-1093-7","article-title":"Monitoring Cancer Prognosis, Diagnosis and Treatment Efficacy Using Metabolomics and Lipidomics","volume":"12","author":"Armitage","year":"2016","journal-title":"Metabolomics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1038\/s41581-021-00488-2","article-title":"Lipidomic Approaches to Dissect Dysregulated Lipid Metabolism in Kidney Disease","volume":"18","author":"Baek","year":"2022","journal-title":"Nat. Rev. Nephrol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/s0039-128x(00)00140-9","article-title":"Allopregnanolone, Pregnenolone Sulfate, and Epitestosterone in Breast Cyst Fluid","volume":"66","author":"Bic\u00edkov\u00e1","year":"2001","journal-title":"Steroids"},{"key":"B6","doi-asserted-by":"publisher","first-page":"7515","DOI":"10.1021\/acs.analchem.9b05765","article-title":"Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics","volume":"92","author":"Bonini","year":"2020","journal-title":"Anal. Chem."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1007\/s11306-015-0809-4","article-title":"An Integrated Targeted Metabolomic Platform for High-Throughput Metabolite Profiling and Automated Data Processing","volume":"11","author":"Cai","year":"2015","journal-title":"Metabolomics"},{"key":"B8","doi-asserted-by":"publisher","first-page":"e0190958","DOI":"10.1371\/journal.pone.0190958","article-title":"Multiplatform Plasma Metabolic and Lipid Fingerprinting of Breast Cancer: a Pilot Control-Case Study in Colombian Hispanic Women","volume":"13","author":"Cala","year":"2018","journal-title":"PLoS One"},{"key":"B9","doi-asserted-by":"publisher","first-page":"101092","DOI":"10.1016\/j.plipres.2021.101092","article-title":"Dissecting Lipid Metabolism Alterations in SARS-CoV-2","volume":"82","author":"Casari","year":"2021","journal-title":"Prog. Lipid Res."},{"key":"B10","doi-asserted-by":"publisher","first-page":"1377","DOI":"10.1038\/s41592-021-01303-3","article-title":"Metabolite Discovery through Global Annotation of Untargeted Metabolomics Data","volume":"18","author":"Chen","year":"2021","journal-title":"Nat. Methods"},{"key":"B11","doi-asserted-by":"publisher","first-page":"438","DOI":"10.3322\/caac.21583","article-title":"Breast Cancer Statistics, 2019","volume":"69","author":"DeSantis","year":"2019","journal-title":"CA Cancer J. Clin."},{"key":"B12","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/j.jpba.2018.10.047","article-title":"Altered Profiles and Metabolism of L- and D-Amino Acids in Cultured Human Breast Cancer Cells vs. Non-tumorigenic Human Breast Epithelial Cells","volume":"164","author":"Du","year":"2019","journal-title":"J. Pharm. Biomed. Anal."},{"key":"B13","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1038\/s41587-020-0740-8","article-title":"Systematic Classification of Unknown Metabolites Using High-Resolution Fragmentation Mass Spectra","volume":"39","author":"D\u00fchrkop","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1016\/j.clnesp.2021.09.006","article-title":"Docosahexaenoic Acid (DHA) and Linoleic Acid (LA) Modulate the Expression of Breast Cancer Involved miRNAs in MDA-MB-231 Cell Line","volume":"46","author":"Elieh Ali Komi","year":"2021","journal-title":"Clin. Nutr. ESPEN"},{"key":"B15","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1159\/000430844","article-title":"Metabolomics Biomarkers for Breast Cancer","volume":"82","author":"G\u00fcnther","year":"2015","journal-title":"Pathobiology"},{"key":"B16","doi-asserted-by":"publisher","first-page":"123069","DOI":"10.1016\/j.jchromb.2021.123069","article-title":"Current State-Of-The-Art of Separation Methods Used in LC-MS Based Metabolomics and Lipidomics","volume":"1188","author":"Harrieder","year":"2022","journal-title":"J. Chromatogr. B"},{"key":"B17","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.jmsacl.2021.10.001","article-title":"A Pilot Study Optimizing Metabolomic and Lipidomic Acquisition in Serum for Biomarker Discovery in Nonalcoholic Fatty Liver Disease","volume":"22","author":"He","year":"2021","journal-title":"J. Mass Spectrom. Adv. Clin. Lab."},{"key":"B18","doi-asserted-by":"publisher","first-page":"5927","DOI":"10.1007\/s00216-021-03425-1","article-title":"Advanced Tandem Mass Spectrometry in Metabolomics and Lipidomics-Methods and Applications","volume":"413","author":"Heiles","year":"2021","journal-title":"Anal. Bioanal. Chem."},{"key":"B19","doi-asserted-by":"publisher","first-page":"113531","DOI":"10.1016\/j.jpba.2020.113531","article-title":"An Improved Detection and Identification Strategy for Untargeted Metabolomics Based on UPLC-MS","volume":"191","author":"Hou","year":"2020","journal-title":"J. Pharm. Biomed. Anal."},{"key":"B20","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.jchromb.2018.11.029","article-title":"Breast Cancer Detection Using Targeted Plasma Metabolomics","volume":"1105","author":"Jasbi","year":"2019","journal-title":"J. Chromatogr. B Anal. Technol. Biomed. Life Sci."},{"key":"B21","doi-asserted-by":"publisher","first-page":"e1900042","DOI":"10.1002\/pmic.201900042","article-title":"Challenges and Opportunities in Cancer Metabolomics","volume":"19","author":"Kumar","year":"2019","journal-title":"Proteomics"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1338","DOI":"10.1373\/clinchem.2012.200527","article-title":"Fasting Serum Lipid and Dehydroepiandrosterone Sulfate as Important Metabolites for Detecting Isolated Postchallenge Diabetes: Serum Metabolomics via Ultra-high-performance LC-MS","volume":"59","author":"Liu","year":"2013","journal-title":"Clin. Chem."},{"key":"B23","doi-asserted-by":"publisher","first-page":"114058","DOI":"10.1016\/j.jpba.2021.114058","article-title":"Serum Untargeted Metabolomics Delineates the Metabolic Status in Different Subtypes of Non-alcoholic Fatty Liver Disease","volume":"200","author":"Liu","year":"2021","journal-title":"J. Pharm. Biomed. Anal."},{"key":"B24","doi-asserted-by":"publisher","first-page":"114134","DOI":"10.1016\/j.jpba.2021.114134","article-title":"Metabolomics-guided Global Pathway Analysis Reveals Better Insights into the Metabolic Alterations of Breast Cancer","volume":"202","author":"Long","year":"2021","journal-title":"J. Pharm. Biomed. Anal."},{"key":"B25","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.ctrv.2018.04.012","article-title":"Metabolomics in Breast Cancer: A Decade in Review","volume":"67","author":"McCartney","year":"2018","journal-title":"Cancer Treat. Rev."},{"key":"B26","doi-asserted-by":"publisher","first-page":"10075","DOI":"10.1021\/acs.analchem.1c00767","article-title":"Simultaneous 3-Nitrophenylhydrazine Derivatization Strategy of Carbonyl, Carboxyl and Phosphoryl Submetabolome for LC-MS\/MS-Based Targeted Metabolomics with Improved Sensitivity and Coverage","volume":"93","author":"Meng","year":"2021","journal-title":"Anal. Chem."},{"key":"B27","doi-asserted-by":"publisher","first-page":"115324","DOI":"10.1016\/j.trac.2018.11.022","article-title":"From Mass to Metabolite in Human Untargeted Metabolomics: Recent Advances in Annotation of Metabolites Applying Liquid Chromatography-Mass Spectrometry Data","volume":"120","author":"Nash","year":"2019","journal-title":"TrAC Trends Anal. Chem."},{"key":"B28","doi-asserted-by":"publisher","first-page":"e0225129","DOI":"10.1371\/journal.pone.0225129","article-title":"Plasma Metabolites as Possible Biomarkers for Diagnosis of Breast Cancer","volume":"14","author":"Park","year":"2019","journal-title":"PLoS One"},{"key":"B29","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/j.aca.2018.04.027","article-title":"Exploring the Potential of Needle Trap Microextraction Combined with Chromatographic and Statistical Data to Discriminate Different Types of Cancer Based on Urinary Volatomic Biosignature","volume":"1023","author":"Porto-Figueira","year":"2018","journal-title":"Anal. Chim. Acta"},{"key":"B30","doi-asserted-by":"publisher","first-page":"Unit 30.2.1","DOI":"10.1002\/0471142727.mb3002s98","article-title":"Targeted Metabolomics","author":"Roberts","year":"2012","journal-title":"Curr. Protoc. Mol. Biol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"102","DOI":"10.3390\/metabo9050102","article-title":"Breast Cancer Metabolomics: from Analytical Platforms to Multivariate Data Analysis. A Review","volume":"9","author":"Silva","year":"2019","journal-title":"Metabolites"},{"key":"B32","doi-asserted-by":"publisher","first-page":"5842","DOI":"10.1038\/s41467-020-19694-w","article-title":"Proto-oncogene Src Links Lipogenesis via Lipin-1 to Breast Cancer Malignancy","volume":"11","author":"Song","year":"2020","journal-title":"Nat. Commun."},{"key":"B33","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1016\/j.molonc.2014.07.012","article-title":"Serum Metabolomic Profiles Evaluated after Surgery May Identify Patients with Oestrogen Receptor Negative Early Breast Cancer at Increased Risk of Disease Recurrence. Results from a Retrospective Study","volume":"9","author":"Tenori","year":"2015","journal-title":"Mol. Oncol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"11835","DOI":"10.1021\/ac402526c","article-title":"High-Throughput LC-MS\/MS Based Simultaneous Determination of Polyamines Including N-Acetylated Forms in Human Saliva and the Diagnostic Approach to Breast Cancer Patients","volume":"85","author":"Tsutsui","year":"2013","journal-title":"Anal. Chem."},{"key":"B35","doi-asserted-by":"publisher","first-page":"3512","DOI":"10.1021\/acs.analchem.7b05355","article-title":"Comprehensive Profiling of Fecal Metabolome of Mice by Integrated Chemical Isotope Labeling-Mass Spectrometry Analysis","volume":"90","author":"Yuan","year":"2018","journal-title":"Anal. Chem."},{"key":"B36","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1038\/nprot.2012.024","article-title":"A Positive\/negative Ion-Switching, Targeted Mass Spectrometry-Based Metabolomics Platform for Bodily Fluids, Cells, and Fresh and Fixed Tissue","volume":"7","author":"Yuan","year":"2012","journal-title":"Nat. Protoc."},{"key":"B37","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/j.talanta.2016.04.049","article-title":"Untargeted Saliva Metabonomics Study of Breast Cancer Based on Ultra Performance Liquid Chromatography Coupled to Mass Spectrometry with HILIC and RPLC Separations","volume":"158","author":"Zhong","year":"2016","journal-title":"Talanta"},{"key":"B38","doi-asserted-by":"publisher","first-page":"6362","DOI":"10.1039\/c6an01753c","article-title":"Strategies for Large-Scale Targeted Metabolomics Quantification by Liquid Chromatography-Mass Spectrometry","volume":"141","author":"Zhou","year":"2016","journal-title":"Analyst"}],"container-title":["Frontiers in Pharmacology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphar.2022.894099\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,30]],"date-time":"2022-05-30T06:45:15Z","timestamp":1653893115000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphar.2022.894099\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,30]]},"references-count":38,"alternative-id":["10.3389\/fphar.2022.894099"],"URL":"https:\/\/doi.org\/10.3389\/fphar.2022.894099","relation":{},"ISSN":["1663-9812"],"issn-type":[{"value":"1663-9812","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5,30]]},"article-number":"894099"}}