Current trends and challenges in sample preparation for global metabolomics using liquid chromatography–mass spectrometry

Abstract

The choice of sample-preparation method is extremely important in metabolomic studies because it affects both the observed metabolite content and biological interpretation of the data. An ideal sample-preparation method for global metabolomics should (i) be as non-selective as possible to ensure adequate depth of metabolite coverage; (ii) be simple and fast to prevent metabolite loss and/or degradation during the preparation procedure and enable high-throughput; (iii) be reproducible; and (iv) incorporate a metabolism-quenching step to represent true metabolome composition at the time of sampling. Despite its importance, sample preparation is often an overlooked aspect of metabolomics, so the focus of this review is to explore the role, challenges, and trends in sample preparation specifically within the context of global metabolomics by liquid chromatography-mass spectrometry (LC-MS). This review will cover the most common methods including solvent precipitation and extraction, solid-phase extraction and ultrafiltration, and discuss how to improve analytical quality and metabolite coverage in metabolomic studies of biofluids, tissues, and mammalian cells. Recent developments in this field will also be critically examined, including in vivo methods, turbulent-flow chromatography, and dried blood spot sampling.

Pre-analytic evaluation of volumetric absorptive microsampling and integration in a mass spectrometry-based metabolomics workflow

“…Moreover, extraction protocols are sample dependent [29,30], and specific extraction procedures are recommended for cells [31], serum [18], urine [32], and dried blood spots [15,33], respectively.…”

Postgenomics Diagnostics: Metabolomics Approaches to Human Blood Profiling

“…This is generally accomplished by using the simplest sample preparation procedures, such as dilution, solvent precipitation, or solvent extraction. More selective procedures, such as liquid-liquid extraction, are usually avoided in metabolomics studies (Tulipani et al, 2013;Vuckovic, 2012). Deproteinization is the minimum sample treatment required prior to MS analysis of blood metabolites and is commonly achieved using organic solvent precipitation (Bruce SJ et al, 2009), protein denaturation, or ultrafiltration (Psychogios et al, 2011).…”

“…Deproteinization is the minimum sample treatment required prior to MS analysis of blood metabolites and is commonly achieved using organic solvent precipitation (Bruce SJ et al, 2009), protein denaturation, or ultrafiltration (Psychogios et al, 2011). Protein precipitation with an organic solvent is the most commonly used method in the global metabolomics of blood (Vuckovic, 2012). In addition to protein removal, the addition of an organic solvent to biofluid also disrupts any bindings between metabolites and proteins present in solution, and thus allows for an analysis of bound and unbound (free) blood metabolites.…”

La métabolomique au service de la médecine

“…Au-delà de la simple description des profils métabolomiques dans cette Si la chromatographie en phase gazeuse permet l'identification de composés volatiles, les métabolites analysés avec cette technique doivent également être thermostables et non polaires, proprié-tés qui limitent le nombre de molécules identifiables [8]. Au contraire, la chromatographie en phase liquide sépare les molécules analysées en fonction de leurs propriétés physicochimiques, telles que la polarité, la charge ionique et le poids moléculaire [9]. De plus, de nombreuses librairies de composés associés à la chromatographie en phase gazeuse sont disponibles, au contraire de la chromatographie en phase liquide pour laquelle peu de banques de données consultables sont disponibles pour le moment.…”