Authors: J A Kirwan D I Broadhurst R L Davidson M R Viant
Publish Date: 2013/03/01
Volume: 405, Issue: 15, Pages: 5147-5157
Abstract
Direct infusion mass spectrometry DIMSbased untargeted metabolomics measures many hundreds of metabolites in a single experiment While every effort is made to reduce withinexperiment analytical variation in untargeted metabolomics unavoidable sources of measurement error are introduced This is particularly true for largescale multibatch experiments necessitating the development of robust workflows that minimise batchtobatch variation Here we conducted a purposedesigned eightbatch DIMS metabolomics study using nanoelectrospray nESI Fourier transform ion cyclotron resonance mass spectrometric analyses of mammalian heart extracts First we characterised the intrinsic analytical variation of this approach to determine whether our existing workflows are fit for purpose when applied to a multibatch investigation Batchtobatch variation was readily observed across the 7day experiment both in terms of its absolute measurement using quality control QC and biological replicate samples as well as its adverse impact on our ability to discover significant metabolic information within the data Subsequently we developed and implemented a computational workflow that includes totalioncurrent filtering QCrobust spline batch correction and spectral cleaning and provide conclusive evidence that this workflow reduces analytical variation and increases the proportion of significant peaks We report an overall analytical precision of 159 measured as the median relative standard deviation RSD for the technical replicates of the biological samples across eight batches and 7 days of measurements When compared against the FDA guidelines for biomarker studies which specify an RSD of 20 as an acceptable level of precision we conclude that our new workflows are fit for purpose for largescale highthroughput nESI DIMS metabolomics studiesThis work was in part supported by the UK Natural Environmental Research Council NERC Biomolecular Analysis Facility at the University of Birmingham R8H1061 and by the British Heart Foundation The FTICR used in this research was obtained through the Birmingham Science City Translational Medicine Experimental Medicine Network of Excellence project with support from Advantage West Midlands AWM David Broadhurst holds salary support from Pfizer Canada We thank Leansale Ltd Abattoir Birmingham for donating the hearts and Tristan Payne for providing MATLAB programming support
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