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Laser Desorption/Ionization Mass Spectrometry on Porous Silicon for Metabolome Analyses: Influence of Surface Oxidation

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Laser Desorption/Ionization Mass Spectrometry on Porous Silicon for Metabolome Analyses: Influence of Surface Oxidation RAPID COMMUNICATIONS IN MASS SPECTROMETRY Rapid Commun. Mass Spectrom. 2007; 21: 2157–2166 Published online in Wiley InterScience (www.interscience.wiley.com) DOI: 10.1002/rcm.3078 Laser desorption/ionization mass spectrometry on porous silicon for metabolome analyses: influence of surface oxidation Seetharaman Vaidyanathan1*,y, Dan Jones3, Joanne Ellis1, Tudor Jenkins3, Chin Chong2, Mike Anderson2 and Royston Goodacre1 1School of Chemistry, Manchester Interdisciplinary Biocentre, The University of Manchester, 131, Princess Street, Manchester M1 7DN, UK 2School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9LP, UK 3Institute of Physical and Mathematical Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3BZ, UK Received 21 December 2006; Revised 4 April 2007; Accepted 1 May 2007 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 positive- ion 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 vibrational spectroscopic techniques including Fourier trans- the metabolome (intermediates of metabolism generally form infrared (FT-IR) and Raman spectroscopies.16 considered to be small molecular weight species) have a An ideal requirement for profiling on a metabolome scale significant role in functional genomic investigations, and is to keep the sample processing steps minimal and develop in turn in our understanding of biological systems.1–5 These simple and rational protocols, not only for ease of operation analyses typically involve large-scale high-throughput screen- when dealing with many samples, but also because this will ing of many analytes simultaneously, and include determining minimize sample intervention (e.g., no chemical derivatiza- changes (ideally quantitatively) in the metabolite profiles of tion needed) and keep the analysis times within manage- the intracellular6 and extracellular7,8 matrices. To fulfill these able limits for high-throughput metabolite profiling. Mass requirements several approaches are being investigated,5,9,10 spectrometry (MS) offers the spectral resolution required for including methods based on hyphenated techniques, such monitoring multiple analytes. Desorption/ionization mass as chromatographic (GC,11 LC12) or electrophoretic (CE)6,13 spectrometry has been practiced in various forms over the separations followed by mass spectrometry. Other tech- years. In its more recent form, matrix-assisted laser niques being studied for the purpose include two-dimensional desorption/ionization (MALDI)-MS is a popular technique (2D) thin-layer chromatography,14 NMR spectroscopy15 and for the analysis of large (>500 m/z) biopolymers such as peptides, proteins and oligonucleotides. Although not as *Correspondence to: S. Vaidyanathan, Manchester Interdisciplin- popular, its application has also been extended to the ary Biocentre, The University of Manchester, 131, Princess Street, detection of lower molecular weight compounds.17 Its ‘soft’ Manchester M1 7DN, UK. E-mail: [email protected] ionization characteristic is attractive for detecting protonated y Present Address: School of Chemical Engineering and Analyti- cal Sciences, Manchester Interdisciplinary Biocentre, The Uni- versity of Manchester, 131 Princess Street, Manchester M1 7DN, UK. Contract/grant sponsor: BBSRC, UK. Copyright # 2007 John Wiley & Sons, Ltd. 2158 S. Vaidyanathan et al. or deprotonated molecules in preference to fragments, synthetic cocktails, and studied consistency of changes in commonly detected in traditional MS using other ionization the spectral information with changes in the analyte methods. In addition, the propensity to generate singly concentrations. We discuss our observations and the charged species, better tolerance than electrospray ionization suitability of these approaches for metabolomic investi- (ESI)-MS to interference from salts and buffers, and gations. simplicity of sample preparation, makes MALDI-MS ideally suited for simultaneous, rapid, high-throughput analyses of EXPERIMENTAL metabolites in complex biological mixtures, such as would be encountered in metabolomic investigations. Materials However, the employment of an organic matrix, as is the Two cocktails, one consisting of 30 metabolites and the other requirement in conventional MALDI-MS, results in inter- 20 metabolites, were used in the study. Cocktail A consisted ference from matrix peaks in the low-mass range. To counter of the amino acids (all in L-form, with shorthand notations – this problem several strategies have been investigated. These used in figures – given in parentheses) alanine (Ala), arginine include the use of high molecular weight compounds as (Arg), asparagine (Asn), cysteine (Cys), glutamine (Gln), matrices,18,19 derivatization of analytes,20 and employment glycine (Gly), histidine (His), isoleucine (Ile), leucine (Leu), of post-source decay (PSD) to reduce interferences from lysine (Lys), methionine (Met), phenylalanine (Phe), proline matrix ions.21 In addition, it has been shown that the (Pro), serine (Ser), threonine (Thr), valine (Val), aspartate employment of lower than conventional matrix-to-analyte (Asp), glutamate (Glu), tryptophan (Trp), tyrosine (Tyr), the molar ratios is an effective means of suppressing matrix organic acids fumarate (Fum), citrate (Cit), malate (Mal), signals.22 However, it has also been noted that the appli- lactate (Lac), pyruvate (Pyr), succinate (deuteriated form – cation of the strategy to analyze multiple compounds in d4-succinate) (d4-Suc), oxaloacetate (Oaa), and the metab- mixtures is limited by analyte ion suppression effects.23 olites 4-aminobutyric acid (Aba), putrescine (Put) and In an alternative approach, Siuzdak and coworkers have D-glucose (G). The above metabolites were present at an pioneered the development of porous silicon as the substrate equimolar concentration of 50 pmol/mL each. Cocktail B for ‘soft’ laser desorption/ionization mass spectrometry;24–27 consisted of the 20 amino acids, 19 of which were at 50 pmol/ a technique termed desorption ionization on porous silicon mL and the 20th (histidine, unless specified otherwise) varied (DIOS). DIOS has been shown to be effective in generating by dilutions such that it was present in the mixture at ‘clean’ spectra of low molecular weight compounds without concentrations of 1 pmol/mLto1mmol/mL. All the metab- complications from matrix peaks. It has also been shown olites were obtained from Sigma-Aldrich (Dorset, UK), and that the information derived can be quantitatively inter- were dissolved in distilled, deionized water (18 Mohms-cm preted.28,29 Although the mechanism of DIOS is not entirely resistivity). understood, preliminary investigations point to the impor- tance of surface morphology. Pore size and surface porosity Porous silicon chips have been found to correlate with improved performance Porous silicon target chips (n-type, 100 orientation) etched in DIOS,25,30–32 as does solvent-surface wetting character- in-house were used in the study. The etching conditions used istics;32 crystal orientation and photoluminescence do not for the in-house preparation were as follows: current 6 mA/ seem to influence DIOS performance.30,32 It has also been cm2 for 2 min in a mixture of hydrofluoric acid and ethanol noted that although a porous surface per se is not required for (1:1). For the generation of oxidized layers the chip was laser desorption in DIOS, a thick porous layer substantially further surface oxidized by exposure to ozone (Ozomax Ltd, improves the analyte ion signal, possibly by resupplying the Quebec, Canada) for 3 min. A commercial DIOS porous surface with analyte after a laser pulse.33 silicon target chip (Mass Consortium Inc., USA) was also Porous silicon surfaces are oxidized when stored in air for used in the study to assess quantitative determinations. extended periods of time34 or on brief exposure to ozone35 or aqueous hydrogen peroxide,36 which have been reported Raman spectroscopy to result in poor
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