Laser desorption/ionization mass spectrometry (LDI-MS) on porous silicon is a promising analytical strategy for the rapid detection of metabolites in biological matrices. We show that both oxidized and unoxidized porous silicon surfaces are useful in detecting protonated/deprotonated molecules from compounds when analyzed in mixtures. We demonstrate the feasibility of using this technique for the simultaneous detection of multiple analytes using a synthetic cocktail of 30 compounds commonly associated with prokaryotic and eukaryotic primary metabolism. The predominantly detected species were the protonated molecules or their sodium/potassium adducts in the positiveion mode and the deprotonated molecules in the negative-ion mode, as opposed to fragments or other adducts. Surface oxidation appears to influence mass spectral responses; in particular, in the mixture we studied, the signal intensities of the hydrophobic amino acids were noticeably reduced. We show that whilst quantitative changes in individual analytes can be detected, ion suppression effects interfere when analyte levels are altered significantly. However, the response of most analytes was relatively unaffected by changes in the concentration of one of the analytes, so long as it was not allowed to dominate the mixture, which may limit the dynamic range of this approach. The differences in the response of the analytes when analyzed in mixtures could not be accounted for by considering their gas-phase and aqueous basicities alone. The implications of these findings in using the technique for metabolome analyses are discussed. Copyright # 2007 John Wiley & Sons, Ltd.There is an increasing realization that analyses characterizing the metabolome (intermediates of metabolism generally considered to be small molecular weight species) have a significant role in functional genomic investigations, and in turn in our understanding of biological systems. 1-5 These analyses typically involve large-scale high-throughput screening of many analytes simultaneously, and include determining changes (ideally quantitatively) in the metabolite profiles of the intracellular 6 and extracellular 7,8 matrices. To fulfill these requirements several approaches are being investigated, 5,9,10 including methods based on hyphenated techniques, such as chromatographic (GC, 11 LC 12 ) or electrophoretic (CE) 6,13 separations followed by mass spectrometry. Other techniques being studied for the purpose include two-dimensional (2D) thin-layer chromatography, 14 NMR spectroscopy 15 and vibrational spectroscopic techniques including Fourier transform infrared (FT-IR) and Raman spectroscopies. 16 An ideal requirement for profiling on a metabolome scale is to keep the sample processing steps minimal and develop simple and rational protocols, not only for ease of operation when dealing with many samples, but also because this will minimize sample intervention (e.g., no chemical derivatization needed) and keep the analysis times within manageable limits for high-throughput metabolite profi...

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