Procedures for large-scale metabolic profiling of serum and plasma using liquid chromatography coupled to mass spectrometry v1

Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography–mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying ultraperformance liquid chromatography–MS (UPLC-MS) are described. These include sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control–based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described.