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Accurate reconstruction of metabolic pathways is an important prerequisite for interpreting metabolomics changes and understanding the diverse biological processes in disease models. A tracer-based metabolomics strategy utilizes stable isotope-labeled precursors to resolve complex pathways by tracing the labeled atom(s) to downstream metabolites through enzymatic reactions. Isotope enrichment analysis is informative and achieved by counting total labeled atoms and acquiring the mass isotopologue distribution (MID) of the intact metabolite. However, quantitative analysis of labeled metabolite substructures/moieties (MS 2 fragments) can offer more valuable insights into the reaction connections through measuring metabolite transformation. In order to acquire the isotopic labeling information at the intact metabolite and moiety level simultaneously, we developed a method that couples hydrophilic interaction liquid chromatography (HILIC) with Zeno trap-enabled high-resolution multiple reaction monitoring (MRM HR ). The method enabled accurate and reproducible MID quantification for intact metabolites as well as their fragmented moieties, with notably high sensitivity in the MS 2 fragmentation mode based on the measurement of 13 C- or 15 N-labeled cellular samples. The method was applied to human-induced pluripotent stem cell-derived neurons to trace the fate of 13 C/ 15 N atoms from D- 13 C 6 -glucose/L- 15 N 2 -glutamine added to the media. With the MID analysis of both intact metabolites and fragmented moieties, we validated the pathway reconstruction of de novo glutathione synthesis in mid-brain neurons. We discovered increased glutathione oxidization from both basal and newly synthesized glutathione pools under neuronal oxidative stress. Furthermore, the significantly decreased de novo glutathione synthesis was investigated and associated with altered activities of several key enzymes, as evidenced by suppressed glutamate supply via glucose metabolism and a diminished flux of glutathione synthetic reaction in the neuronal model of rotenone-induced neurodegeneration.

Carotenoids are natural pigments with provitamin A and antioxidant activities. Biosynthesized in plants as their all-trans isomers, carotenoids isomerize in solution and in humans to multiple cis isomers which can have different bioavailabilities and functions. Since separation and characterization of isomeric carotenoids using high-pressure liquid chromatography (HPLC) or liquid chromatography-tandem mass spectrometry (LC-MS/MS) is time-consuming, the potential for ion mobility mass spectrometry (IM-MS) to resolve and characterize carotenoid isomers rapidly without chromatography was investigated using traveling-wave ion mobility spectrometry on a quadrupole time-of-flight mass spectrometer. The all-trans isomers of lycopene and β-carotene were separated by several milliseconds from the cis-isomers which were detected as partially overlapping peaks. The collision cross-section values of these carotenoid isomers were determined using IM-MS to be 180 and 236 Å(2) for cis-lycopene and all-trans-lycopene, and 181 and 225 Å(2) for cis-β-carotene and all-trans-β-carotene, respectively. Collision-induced dissociation MS/MS of ion mobility-resolved isomers indicated that cis and all-trans carotenoid isomers can be distinguished by their fragmentation patterns. Previous MS/MS studies of cis- and all trans-carotenoids had suggested that they produced identical tandem mass spectra, but this appears to have been the result of isomerization during ionization. Introduction of specific cis or trans isomers by infusion or HPLC resulted in cis/trans isomerization in the ion source during electrospray, and the relative levels of cis carotenoids forming in the ion source compared to the all-trans isomers were temperature dependent.

The use of a combination of ultraperformance liquid chromatography at approximately 11,000 psi on sub 2-microm particles combined with reversed-phase gradient chromatography at a temperature of 90 degrees C is described as applied to the analysis of endogenous and drug metabolites in human and animal urine. By using elevated temperatures, back pressures can be reduced while maintaining high flow rates and chromatographic efficiency, with peaks 1-3 s wide at the base. Application to urine samples provided a peak capacity of approximately 700 for a 10-min analysis and greater than approximately 1000 in 1 h. Despite the narrow nature of the peaks, good quality mass spectra were also obtained, allowing the identification of typical drug and endogenous metabolites. These ultra-high-resolution chromatograms should be ideal for the analysis of complex samples in, for example, metabolite identification, impurity identification, and metabonomic/metabolomic studies. Applications in natural product analysis and proteomics can also be envisaged.

The use of HPLC coupled to inductively coupled plasma mass spectrometry (ICPMS) and orthogonal acceleration time-of-flight (oa-TOF) for the profiling, identification, and quantification of metabolites in rat urine following the administration of 2-bromo-4-trifluoromethylacetanilide is described. The metabolites present in the sample were separated by reversed-phase gradient chromatography with UV-diode array detection. The bulk of the eluent (90%) from the UV detector was directed to an ICPMS where bromine-containing metabolites were detected and quantified using ICPMS. The minor portion of the eluent (10%) was taken for oa-TOFMS for identification. By these means, the metabolites were identified as sulfate and glucuronide conjugates of a ring hydroxy-substituted metabolite, a N-sulfate, a N-hydroxylamine glucuronide, and N- and N-hydroxyglucuronides.