Endogenous metabolites have gained increasing interest over the past 5 years largely for their implications in diagnostic and pharmaceutical biomarker discovery. METLIN (http://metlin.scripps.edu), a freely accessible web-based data repository, has been developed to assist in a broad array of metabolite research and to facilitate metabolite identification through mass analysis. METLINincludes an annotated list of known metabolite structural information that is easily cross-correlated with its catalogue of high-resolution Fourier transform mass spectrometry (FTMS) spectra, tandem mass spectrometry (MS/MS) spectra, and LC/MS data.

The aim of metabolite profiling is to monitor all metabolites within a biological sample for applications in basic biochemical research as well as pharmacokinetic studies and biomarker discovery. Here, novel data analysis software, XCMS, was used to monitor all metabolite features detected from an array of serum extraction methods, with application to metabolite profiling using electrospray liquid chromatography/mass spectrometry (ESI-LC/MS). The XCMS software enabled the comparison of methods with regard to reproducibility, the number and type of metabolite features detected, and the similarity of these features between different extraction methods. Extraction efficiency with regard to metabolite feature hydrophobicity was examined through the generation of unique feature density distribution plots, displaying feature distribution along chromatographic time. Hierarchical clustering was performed to highlight similarities in the metabolite features observed between the extraction methods. Protein extraction efficiency was determined using the Bradford assay, and the residual proteins were identified using nano-LC/MS/MS. Additionally, the identification of four of the most intensely ionized serum metabolites using FTMS and tandem mass spectrometry was reported. The extraction methods, ranging from organic solvents and acids to heat denaturation, varied widely in both protein removal efficiency and the number of mass spectral features detected. Methanol protein precipitation followed by centrifugation was found to be the most effective, straightforward, and reproducible approach, resulting in serum extracts containing over 2000 detected metabolite features and less than 2% residual protein. Interestingly, the combination of all approaches produced over 10,000 unique metabolite features, a number that is indicative of the complexity of the human metabolome and the potential of metabolomics in biomarker discovery.

According to the World Health Organization, cataracts account for half of the blindness in the world, with the majority occurring in developing countries. A cataract is a clouding of the lens of the eye due to light scattering of precipitated lens proteins or aberrant cellular debris. The major proteins in the lens are crystallins and they are extensively deamidated during aging and cataracts. Deamidation has been detected at the domain and monomer interfaces of several crystallins during aging.The purpose of this study was to determine the effects of two potential deamidation sites at the predicted interface of the βA3-crystallin dimer on its structure and stability. The glutamine residues at the reported in vivo deamidation sites of Q180 in the C-terminal domain and at the homologous site Q85 in the N-terminal domain were substituted with glutamic acid residues by site-directed mutagenesis. Far UV and near UV circular dichroism spectroscopy indicated that there were subtle differences in the secondary structure and more notable differences in the tertiary structure of the mutant proteins compared to wild type βA3-crystallin. The Q85E/Q180E mutant also was more susceptible to enzymatic digestion, suggesting increased solvent accessibility. These structural changes in the deamidated mutants led to decreased stability during unfolding in urea and increased precipitation during heat-denaturation. When simulating deamidation at both residues, there was a further decrease in stability and loss of cooperativity. However, multiangle-light scattering and quasielastic light scattering experiments showed that dimer formation was not disrupted, nor did higherorder oligomers form. These results suggest that introducing charges at the predicted domain interface in the βA3 homodimer may contribute to the insolubilization of lens crystallins or favor other, more stable, crystallin subunit interactions.Cataracts account for half of all blindness according to the World Health Organization (1). The greatest incidence is in developing countries. A cataract is opacity within the lens of the eye due to scattering of light by precipitated proteins or by aberrant cellular debris. The major proteins within the lens belong to the α and β/γ-crystallin families. Protein concentrations can reach 400 mg/mL and above in the center of the lens, and it is their ordered packing that is necessary for transparency (2). There is an extremely low rate of turnover of crystallins in differentiated lens cells. Thus, crystallins accumulate modifications due to environmental and metabolic damage during an individual's entire lifetime. This makes the lens an easily accessible tissue to study the effects of post-translational modifications on protein unfolding and aggregation.The major post-translational modifications in lenses are truncation, methylation, oxidation, disulfide bond formation, advanced glycation end-products and deamidation (3)(4)(5)(6)(7)(8)(9)(10)(11)(12). Of these AUTHOR EMAIL ADDRESS lampik@ohsu.edu. NIH Public Access Author M...

This blood spot assay for 25(OH)D(2) and 25(OH)D(3) provides a convenient and cost-effective alternative to serum assays and can be automated. This may be valuable in large-scale screening for risk of type 1 diabetes, for cardiometabolic risk screening, and for monitoring vitamin D supplementation.