From metabolic profiling to metabolomics: Fifty years of instrumental and methodological improvements

Molecular biology has recently concentrated on the determination of multiple gene-expression changes at the RNA level (transcriptomics), and into determination of multiple protein expression changes (proteomics). Similar developments have been taking place at metabolite small-molecule level, leading to the increasing expansion in studies now termed metabolomics. This approach can be used to provide comprehensive and simultaneous systematic profiling of metabolite levels in biofluids and tissues, and their systematic and temporal changes. Analysis of metabolites is not a new field; long prior to the development of the various ''omics'' approaches, the simultaneous analysis of the plethora of metabolites seen in biological fluids had been carried out largely, but historically it has been limited to relatively small numbers of target analytes. However, the realization that metabolic pathways do not act in isolation but rather as part of an extensive network has led to the need for a more holistic approach to metabolite analysis. The main analytical techniques employed for metabolomics studies are based on NMR spectroscopy and mass spectrometry (MS), that, in turn, can be considered complementary each other. Neverthless, MS measurement following chromatographic separation offers the best combination of sensitivity and selectivity, so it is central to most metabolomics approaches. Either gas chromatography after chemical derivatization, or liquid chromatography (LC), with the newer method of ultrahigh-performance LC being used increasingly, can be adopted. Capillary electrophoresis coupled to MS has also shown some promises. Analyte detection by MS in complex mixtures is not as universal as for NMR and quantitation can be impaired by variable ionization and ion-suppression effects. A LC chromatogram is generated with MS detection, usually using electrospray ionization (ESI), and both positive-and negative-ion chromatograms can be recorded. The utilization of nano-ESI can reduce ionization suppression effects due to the increased ionization efficiency. Mass analyzer able to produce high mass resolution, mass accuracy, and tandem MS, such as quadrupole-time-of-flight (Q-TOF) or high-resolution ion trap instruments, are employed. Direct infusion (DI)-MS/MS using Fourier transform ion cyclotron resonance mass spectrometers provides a sensitive, high-throughput method for metabolic fingerprinting. Unfortunately, DI-MS analysis is particularly susceptible to ionization suppression arising from competitive ionization. In metabolomics, matrix assisted laser desorption-ionization (MALDI) has largely been confined to the targeted analysis of high-molecular weight metabolites due to the substantial signals generated by the matrix in the low-molecular-weight region (<1,000 m/z). Recent advancements in laser desorption techniques include desorptionionization MS from porous silicon chips and matrices that have minimal background signals in the low-molecular-weight region. These offer new opportunities for the utilization of MALDI ionization in metabolite screening and fingerprinting employing MALDI-TOF/TOF. However, the technique is still subject to ion suppression and yields poor quantitative detection. Desorption ESI (DESI), a new ambient, soft-ionization technique that combines features from both ESI and desorption-ionization methods, allows the direct analysis of animal and plant tissues. However, DESI experimental conditions typically require optimization for each sample type, so time must be invested initially in optimizing the experimental parameters. © 2011 by Nova Science Publishers, Inc. All rights reserved.