A multiple ionization mass spectrometry strategy is presented based on the analysis of human serum extracts. Chromatographic separation was interfaced inline with the atmospheric pressure ionization techniques electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) in both positive (+) and negative (-) ionization modes. Furthermore, surface-based matrixassisted laser desorption/ionization (MALDI) and desorption ionization on silicon (DIOS) mass spectrometry were also integrated with the separation through fraction collection and offline mass spectrometry. Processing of raw data using the XCMS software resulted in time-aligned ion features, which are defined as a unique m/z at a unique retention time. The ion feature lists obtained through LC-MS with ESI and APCI interfaces in both ( ionization modes were compared, and unique ion tables were generated. Nonredundant, unique ion features, were defined as mass numbers for which no mass numbers corresponding to [M + H] + , [M -H] -, or [M + Na] + were observed in the other ionization methods at the same retention time. Analysis of the extracted serum using ESI for both (+) and (-) ions resulted in >90% additional unique ions being detected in the (-) ESI mode. Complementing the ESI analysis with APCI resulted in an additional ∼20% increase in unique ions. Finally, ESI/ APCI ionization was combined with fraction collection and offline-MALDI and DIOS mass spectrometry. The parts of the total ion current chromatograms in the LC-MS acquired data corresponding to collected fractions were summed, and m/z lists were compiled and compared to the m/z lists obtained from the DIOS/MALDI spectra. It was observed that, for each fraction, DIOS accounted for ∼50% of the unique ions detected. These results suggest that true global metabolomics will require multiple ionization technologies to address the inherent metabolite diversity and therefore the complexity in and of metabolomics studies. Quantitative global analysis of endogenous metabolites from cells, tissues, fluids or whole organismssmetabolomicssis becoming an integral part of functional genomics efforts 1-3 as well as a tool for finding diagnostic biomarkers. 4-7 From a mass spectrometry ionization point of view, the transcriptome and proteome are relatively homogeneous in their respective physicalchemical composition of 4 and 20 chemical building blocks, whereas vast physical-chemical heterogeneity is contained in the metabolome, where the complexity is dictated at the atomic level presenting diversity similar to that of combinatorial libraries. This diversity makes it especially challenging to gain a comprehensive and quantitative measure of the metabolome. For example, simultaneous separation and mass spectrometric detection of the substrate-product pair fructose and fructose 1-phosphate is not trivial. Nuclear magnetic resonance spectroscopy (NMR) 8 and mass spectrometry (MS) 9,10 have become the primary analytical technologies of metabolomics, where they have a great potential to complement each other. 11 Theoretically, 1 H and 13 C NMR are capable of measuring most aspects of the metabolome, yet the low concentrations (<pM) and the extremely large dynamic range (low abundant signaling compounds to central metabolism carbohydrates), typically encountered in biological systems paire
