We have developed an analytical method, consisting of ion-pair liquid chromatography coupled to electrospray ionization mass spectrometry (IP-LC-ESI-MS), for the simultaneous quantitative analysis of several key classes of polar metabolites, like nucleotides, coenzyme A esters, sugar nucleotides, and sugar bisphosphates. The use of the ion-pair agent hexylamine and optimization of the pH of the mobile phases were critical parameters in obtaining good retention and peak shapes of many of the above-mentioned polar and acidic metabolites that are impossible to analyze using standard reversed-phase LC/MS. Optimum conditions were found when using a gradient from 5 mM hexylamine in water (pH 6.3) to 90% methanol/10% 10 mM ammonium acetate (pH 8.5). The IP-LC-ESI-MS method was extensively validated by determining the linearity (R2 > 0.995), sensitivity (limit of detection 0.1-1 ng), repeatability, and reproducibility (relative standard deviation <10%). The IP-LC-ESI-MS method was shown to be a useful tool for microbial metabolomics, i.e., the comprehensive quantitative analysis of metabolites in extracts of microorganisms, and for the determination of the energy charge, i.e., the cellular energy status, as an overall quality measure for the sample workup and analytical protocols.

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Significant improvements in the absolute detection limits for proteins in matrix-assisted laser desorptiod ionization mass spectrometry (MALDI-MS) are demonstrated by the application of so-called picolitre vials. By the reduction of the sample volume from a few pL down to 250 pL and simultaneous reduction of the sample spot area from a few mm2 down to 0.01 mm2, low attomole detection limits are obtained for bradykinin and cytochrome c. The detection limit in a single-shot mass spectrum of bradykinin is estimated to be as low as 250 zeptomol. These are currently the lowest amounts of protein and the smallest volumes analyzed by MALDI-MS.

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