title: Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry.
abstract: 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 gas chromatography-MS (GC-MS) and ultraperformance liquid chromatography-MS (UPLC-MS) are described. These include biofluid collection, 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.
authors: Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK. warwick.dunn@manchester.ac.uk
authors: Warwick B
authors: WB
authors: Dunn
authors: David
authors: D
authors: Broadhurst
authors: Paul
authors: P
authors: Begley
authors: Eva
authors: E
authors: Zelena
authors: Sue
authors: S
authors: Francis-McIntyre
authors: Nadine
authors: N
authors: Anderson
authors: Marie
authors: M
authors: Brown
authors: Joshau D
authors: JD
authors: Knowles
authors: Antony
authors: A
authors: Halsall
authors: John N
authors: JN
authors: Haselden
authors: Andrew W
authors: AW
authors: Nicholls
authors: Ian D
authors: ID
authors: Wilson
authors: Douglas B
authors: DB
authors: Kell
authors: Royston
authors: R
authors: Goodacre
mesh_terms: D001774:Blood Chemical Analysis; D002853:Chromatography, Liquid / Q000379:methods; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D055432:Metabolomics / Q000379:methods*; D010949:Plasma / Q000737:chemistry; D044967:Serum / Q000737:chemistry