Naama Karu

HMDB 4.0: the human metabolome database for 2018

Abstract The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This years update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB’s chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC–MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.

Determination of pharmaceutically related compounds by suppressed ion chromatography: IV. Interfacing ion chromatography with universal detectors

This work forms the final part of a study investigating gradient elution ion-exchange chromatography of pharmaceutically relevant compounds, aiming at achieving complementary selectivity to reversed-phase HPLC. In this study the coupling of three universal detectors (electro-spray ionisation mass spectrometer (ESI-MS); corona charged aerosol detector (CAD); and evaporative light scattering detector (ELSD)) to suppressed IC using complex elution profiles with potassium hydroxide eluents is demonstrated. The non-volatile ions were removed from the eluent by the suppressor prior to detection, thus allowing a stable detector response, especially with the prototype electrolytic suppressor. The detector response for ten weakly anionic pharmaceuticals followed the expected models and the limits of detection obtained were not compromised by the use of a suppressor, yielding values below 50 ng/mL with MS, low to sub μg/mL levels with CAD and 2-20 μg/mL with ELSD (25 μL injections). When coupled to MS and CAD, the prototype electrolytic suppressor showed percentage relative standard deviations (%RSDs) in peak areas of 0.4-2.5% on average, compared to the chemical suppressor which yielded 1.5-3 fold higher %RSD values for the test analytes. The prototype electrolytic suppressor also generally exhibited wider linear response ranges than the chemical suppressor.

Determination of pharmaceutically related compounds by suppressed ion chromatography: I. Effects of organic solvent on suppressor performance

This overall study aims to investigate gradient elution ion-exchange chromatography of pharmaceutically relevant compounds using universal nebulisation detectors, such as evaporative light scattering detection (ELSD). Addition of organic solvents to the eluent is necessary to minimise hydrophobic adsorption on the polymeric stationary phase and improve solubility of analytes. It is also necessary to de-salt the eluent prior to detection, and in this work, ion chromatography suppressors were used for this step. Such suppressors have been designed for aqueous eluents, so the purpose of the present study was to investigate the effects of methanol and acetonitrile on suppressor performance. Chemical and electrolytic suppressors were evaluated for baseline drift, noise and efficiency of suppression using aqueous/organic eluents containing up to 40% (v/v) methanol or acetonitrile. Chemical suppression of aqueous/organic eluents showed minimal noise levels, uniform low baseline and low gradient drift. Electrolytic suppression gave good performance, but with higher baseline conductivity levels and baseline drift than chemical suppression. The elevated baseline was found not to be caused by incomplete suppression of the eluent, but was attributed to chemical reactions involving the organic solvents and facilitated by high electric currents and heat generation. It was demonstrated that suppressed ion-exchange separation using a complex KOH elution profile could be coupled with ELSD, with the suppressor effectively de-salting the eluent, producing a stable baseline. Finally, complementary separation selectivity was demonstrated using a set of pharmaceutically related organic acids separated by reversed-phase and ion-exchange methods.

YMDB 2.0: a significantly expanded version of the yeast metabolome database.

YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on the genome and metabolome of Saccharomyces cerevisiae. Initially released in 2012, the YMDB has gone through a significant expansion and a number of improvements over the past 4 years. This manuscript describes the most recent version of YMDB (YMDB 2.0). More specifically, it provides an updated description of the database that was previously described in the 2012 NAR Database Issue and it details many of the additions and improvements made to the YMDB over that time. Some of the most important changes include a 7-fold increase in the number of compounds in the database (from 2007 to 16 042), a 430-fold increase in the number of metabolic and signaling pathway diagrams (from 66 to 28 734), a 16-fold increase in the number of compounds linked to pathways (from 742 to 12 733), a 17-fold increase in the numbers of compounds with nuclear magnetic resonance or MS spectra (from 783 to 13 173) and an increase in both the number of data fields and the number of links to external databases. In addition to these database expansions, a number of improvements to YMDBs web interface and its data visualization tools have been made. These additions and improvements should greatly improve the ease, the speed and the quantity of data that can be extracted, searched or viewed within YMDB. Overall, we believe these improvements should not only improve the understanding of the metabolism of S. cerevisiae, but also allow more in-depth exploration of its extensive metabolic networks, signaling pathways and biochemistry.

Simple and robust monitoring of ethanol fermentations by capillary electrophoresis

Free‐solution capillary electrophoresis (CE), or capillary zone electrophoresis, with direct UV detection was used for the first time for the determination of mono‐ and disaccharides, sugar alcohols, and ethanol in fermentation broths. Sample preparation proved to be minimal: no derivatization or specific sample purification was needed. The CE conditions can be adapted to the type of fermentation by simply altering the background electrolyte (BGE). KOH (130 mM) or NaOH (130 mM) as the BGE led to the fastest analysis time when monitoring simple fermentations. A mixture of 65 mM NaOH and 65 mM LiOH led to a 19% improvement in resolution for a complex mixture of carbohydrates. Quantification of a simple carbohydrate fermentation by CE showed values in close agreement with that of high‐performance anion exchange chromatography and high‐performance liquid chromatography (HPLC) on a cation exchange resin. For complex fermentations, quantification of carbohydrates by HPLC and CE led to similar results, whereas CE requires an injection volume of only 10–20 nL. Analysis of an ethanol fermentation of hydrolyzed plant fiber demonstrated the robustness of the separation and detection of carbohydrates, as well as ethanol. Ethanol determination is achieved by coupling the CE method to pressure mobilization, using the same instrument and the same sample.

Determination of pharmaceutically related compounds by suppressed ion chromatography: II. Interactions of analytes with the suppressor

For the hyphenation of ion chromatography to nebulising detectors or mass spectrometry, suppression of the non-volatile ionic eluent to water is a required step. However, suppression of weakly acidic or weakly basic organic analytes can potentially lead to losses of analytes during suppression resulting from precipitation, hydrophobic adsorption onto the suppressor, or permeation of the analyte through the suppressor membranes. This study investigates the interactions between the suppressor and weak organic acid analytes, including pharmaceutically related compounds, for eluents containing organic solvent. Correlations were observed between analyte recovery rates after electrolytic suppression and the eluent composition, the suppression conditions, and the physico-chemical properties of the analytes. These results suggest that hydrophobic adsorption interactions occur in the electrolytic suppressor and that these interactions are ameliorated by the addition to the eluent of high levels of organic solvents, especially acetonitrile. Use of eluents containing 80% acetonitrile resulted in very low losses of analyte during suppression. Recovery experiments conducted in various compartments of the electrolytic suppressor showed that some analytes permeated through the suppressor membrane into the regenerant chambers, but this could be prevented by adding organic solvent to the regenerant solution. It was also noted that analyte losses increased with ageing of the electrolytic suppressors. Chemical suppression avoids some of the analyte losses observed with an electrolytic suppressor, but when used under the correct conditions, electrolytic suppressors gave close to equivalent performance to chemical suppressors.

Determination of pharmaceutically related compounds by suppressed ion chromatography: III. Role of electrolytic suppressor design

For the hyphenation of ion chromatography to nebulising detectors or mass spectrometry, suppression of the non-volatile ionic eluent to water is a required step to avoid elevated detector baselines. Presented here is a study of three new designs of electrolytic suppressors, incorporating high ion-exchange capacity screens and high ion-exchange capacity membranes in different thickness and compositions. These designs aim to minimise hydrophobic interactions of the suppressor with organic analytes and to provide higher compatibility with eluents containing acetonitrile. In comparison with a commercially available electrolytic suppressor and also a commercially available chemical suppressor, the new high-capacity suppressor showed superior performance, exhibiting minimal interactions with a test set of analytes under the examined conditions. This led to the attainment of high recoveries of the analytes after suppression (93-99% recovery) and significantly reduced band broadening during suppression. The new suppressor has been shown to perform well under both isocratic and gradient elution conditions.

A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database

Metabolomic analysis of human biospecimens had progressed quickly over the past decade. Technological and methodological advances have led to the comprehensive characterization of human serum, urine, cerebrospinal fluid and saliva metabolomes, and the creation of freely available metabolome reference databases. Unfortunately, the characterization of the human fecal metabolome still lags behind these other metabolomes in terms of the availability of standardized methods and freely available resources. The purpose of this review is to bring the knowledge of the human fecal metabolome, and the methods to characterize it, to the same level as most other human biofluid metabolomes. More specifically, this review is intended to critically assess the field of fecal metabolomics and to provide a comprehensive review of the current state of knowledge with regard to the protocols, technologies and remaining challenges in fecal metabolite analysis. In addition to providing an overview of fecal metabolomics and some consensus recommendations, we also present the human fecal metabolome database (HFMDB - http://www.fecalmetabolome.ca), a freely available, manually curated resource that currently contains over 6000 identified human fecal metabolites. Each entry in the HFMDB includes extensive chemical information, metabolite descriptions and reference data in the same format as the Human Metabolome Database (HMDB).