Variability Analysis of Human Plasma and Cerebral Spinal Fluid Reveals Statistical Significance of Changes in Mass Spectrometry-Based Metabolomics Data

• Published in: Analytical chemistry (Washington) Vol. 81; no. 20; pp. 8538 - 8544
• Main Authors: Crews, Bridgit, Wikoff, William R, Patti, Gary J, Woo, Hin-Koon, Kalisiak, Ewa, Heideker, Johanna, Siuzdak, Gary
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 15.10.2009
• Subjects: Analysis of Variance; Analytical chemistry; Biological analysis; Biological variation; Biomarkers - blood; Biomarkers - metabolism; Blood Chemical Analysis - methods; Cerebrospinal Fluid - chemistry; Cerebrospinal Fluid - metabolism; Chemistry; Chromatographic methods and physical methods associated with chromatography; Chromatography; Chromatography, Liquid; Coefficient of variation; Comparative analysis; Databases, Factual; Exact sciences and technology; Humans; Liquid chromatography; Mass spectra; Mass Spectrometry; Metabolites; Metabolomics; Nonlinear Dynamics; Other chromatographic methods; Plasma; Principal Component Analysis; Reproducibility of Results; Software; Spectrometric and optical methods; Human; Metabolomics; Peak resolution; Metabolite; Coupled method; Biological marker; Liquid chromatography; Retention time; Reproducibility; Mass spectrometry MS/MS; Robustness; Mass spectrometry; Variation coefficient
• ISSN: 0003-2700; 1520-6882; 1520-6882
• DOI: 10.1021/ac9014947

Analytical and biological variability are issues of central importance to human metabolomics studies. Here both types of variation are examined in human plasma and cerebrospinal fluid (CSF) using a global liquid chromatography/mass spectrometry (LC/MS) metabolomics strategy. The platform shows small analytical variation with a median coefficient of variation (CV) of 15−16% for both plasma and CSF sample matrixes when the integrated area of each peak in the mass spectra is considered. Analysis of biological variation shows that human CSF has a median CV of 35% and plasma has a median CV of 46%. To understand the difference in CV between the biofluids, we compared plasma and CSF independently obtained from different healthy humans. Additionally, we analyzed another group of patients from whom we compared matched CSF and plasma (plasma and CSF obtained from the same human subject). A similar number of features was observed in both biofluids, although the majority of features appeared with greater intensity in plasma. More than a dozen metabolites shared between the human CSF and plasma metabolomes were identified based on accurate mass measurements, retention times, and MS/MS spectra. The fold change in these metabolites was consistent with the median biological CV determined for all peaks. The measured median biological CV together with analysis of intragroup variation of healthy individuals suggests that fold changes above 2 in metabolomics studies investigating plasma or CSF are statistically relevant with respect to the inherent variability of a healthy control group. These data demonstrate the reproducibility of the global metabolomics platform using LC/MS and reveal the robustness of the approach for biomarker discovery.