Untargeted Metabolomics of Urine and Plasma

Untargeted metabolomics from urine and plasma samples collected at 26 months were performed by Metabolon (Raleigh, NC) as previously described [24 (link)]. In brief, all experiments used a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The scan range varied slightly between methods but covered 70-1000 m/z. Raw data were extracted, peak- identified, and processed for quality control using Metabolon’s hardware and software. Compounds were identified by comparison to library entries of purified standards or recurrent unknown entities. Peaks were quantified using area-under-the-curve. The informatics consisted of the Laboratory Information Management System (LIMS), the data extraction and peak-identification software, data processing tools for quality control and compound identification, and a collection of information interpretation and visualization tools for use by data analysts. The hardware and software foundations for these components were the LAN backbone, and a database server running Oracle 10.2.1.1 Enterprise Edition. Values were then log transformed, and missing values, if any, were imputed with the minimum observed value for each compound.