The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users.

Metabolites containing a carbonyl group represent several important classes of molecules including various forms of ketones and aldehydes such as steroids and sugars. We report a high-performance chemical isotope labeling (CIL) LC-MS method for profiling the carbonyl submetabolome with high coverage and high accuracy and precision of relative quantification. This method is based on the use of dansylhydrazine (DnsHz) labeling of carbonyl metabolites to change their chemical and physical properties to such an extent that the labeled metabolites can be efficiently separated by reversed phase LC and ionized by electrospray ionization MS. In the analysis of six standards representing different carbonyl classes, acetaldehyde could be ionized only after labeling and MS signals were significantly increased for other 5 standards with an enhancement factor ranging from ∼15-fold for androsterone to ∼940-fold for 2-butanone. Differential C- andC-DnsHz labeling was developed for quantifying metabolic differences in comparative samples where individual samples were separately labeled with C-labeling and spiked with aC-labeled pooled sample, followed by LC-MS analysis, peak pair picking, and peak intensity ratio measurement. In the replicate analysis of a 1:1 C-/C-labeled human urine mixture (n = 6), an average of 2030 ± 39 pairs per run were detected with 1737 pairs in common, indicating the possibility of detecting a large number of carbonyl metabolites as well as high reproducibility of peak pair detection. The average RSD of the peak pair ratios was 7.6%, and 95.6% of the pairs had a RSD value of less than 20%, demonstrating high precision for peak ratio measurement. In addition, the ratios of most peak pairs were close to the expected value of 1.0 (e.g., 95.5% of them had ratios of between 0.67 and 1.5), showing the high accuracy of the method. For metabolite identification, a library of DnsHz-labeled standards was constructed, including 78 carbonyl metabolites with each containing MS, retention time (RT), and MS/MS information. This library and an online search program for labeled carbonyl metabolite identification based on MS, RT, and MS/MS matches have been implemented in a freely available Website, www.mycompoundid.org . Using this library, out of the 1737 peak pairs detected in urine, 33 metabolites were positively identified. In addition, 1333 peak pairs could be matched to the metabolome databases with most of them belonging to the carbonyl metabolites. These results show that C-/C-DnsHz labeling LC-MS is a useful tool for profiling the carbonyl submetabolome of complex samples with high coverage.

Ab initio calculations were carried out for isogyric reactions involving the third row elements, Ga, Ge, As, Se, and Br. Geometries of all the reactants and products were optimized at the HF, MP2, and B3LYP levels of theory using the 6-31G(d) and 6-31G(d,p) basis sets. For molecules containing third row elements geometries, frequencies and thermodynamic properties were calculated using both the standard 6-31G and the Binning-Curtiss (BC6-31G) basis sets. In order to determine the performance of these basis sets, the calculated thermodynamic properties were compared to G3MP2 values and where possible to experimental values. Geometries and frequencies calculated with the standard 6-31G and the BC6-31G basis sets were found to differ significantly. Frequencies calculated with the standard 6-31G basis set were generally in better agreement with the experimental values (MAD=40.1 cm(-1) at B3LYP/6-31G(d,p) and 94.2 cm(-1) at MP2/6-31G(d,p) for unscaled frequencies and 29.6 cm(-1) and 24.4 cm(-1), respectively, for scaled frequencies). For all the reactions investigated, the thermodynamic properties calculated with the standard 6-31G basis set were found to consistently be in better agreement with the G3MP2 and the available experimental results. However, the BC6-31G basis set performs poorly for the reactions involving both second and third row elements. Since, in general, the standard 6-31G basis set performs well for all the reactions, we recommend that the standard 6-31G basis set be used for calculations involving third row elements. Using G3MP2 enthalpies of reaction and available experimental heats of formation (ΔHf), previously unknown ΔHf for CH3SeH, SiH3SeH, CH3AsH2, SiH3AsH2, CH3GeH3, and SiH3GeH3 were found to be 18.3, 18.0, 38.4, 82.4, 41.9, and 117.4 kJ mol(-1), respectively.