biostudies-literatureShi Zthe National Science Foundation of China1168https://www.ebi.ac.uk/biostudies/studies/S-EPMC9782571biostudies-literatureUnknown12(12)As a comprehensive analysis of all metabolites in a biological system, metabolomics is being widely applied in various clinical/health areas for disease prediction, diagnosis, and prognosis. However, challenges remain in dealing with the metabolomic complexity, massive data, metabolite identification, intra- and inter-individual variation, and reproducibility, which largely limit its widespread implementation. This study provided a comprehensive workflow for clinical metabolomics, including sample collection and preparation, mass spectrometry (MS) data acquisition, and data processing and analysis. Sample collection from multiple clinical sites was strictly carried out with standardized operation procedures (SOP). During data acquisition, three types of quality control (QC) samples were seMetabolitesA Comprehensive Mass Spectrometry-Based Workflow for Clinical Metabolomics Cohort Studies.PMC978257182160553Qing BLi HKang XXia ZWillmitzer LCaldana CShi ZSong GZhang WZeng CLi YHu JChen YXu XYuan YfalseA Comprehensive Mass Spectrometry-Based Workflow for Clinical Metabolomics Cohort Studies.As a comprehensive analysis of all metabolites in a biological system, metabolomics is being widely applied in various clinical/health areas for disease prediction, diagnosis, and prognosis. However, challenges remain in dealing with the metabolomic complexity, massive data, metabolite identification, intra- and inter-individual variation, and reproducibility, which largely limit its widespread implementation. This study provided a comprehensive workflow for clinical metabolomics, including sample collection and preparation, mass spectrometry (MS) data acquisition, and data processing and analysis. Sample collection from multiple clinical sites was strictly carried out with standardized operation procedures (SOP). During data acquisition, three types of quality control (QC) samples were se2022-01-01T00:00:00Z2022 Nov2025-04-18T16:00:02.738Z2025-04-07T02:58:17.42ZS-EPMC97825713655720710.3390/metabo12121168