PlantMAT: A Metabolomics Tool for Predicting the Specialized Metabolic Potential of a System and for Large-Scale Metabolite Identifications.

Custom software entitled Plant Metabolite Annotation Toolbox (PlantMAT) has been developed to address the number one grand challenge in metabolomics, which is the large-scale and confident identification of metabolites. PlantMAT uses informed phytochemical knowledge for the prediction of plant natural products such as saponins and glycosylated flavonoids through combinatorial enumeration of aglycone, glycosyl, and acyl subunits. Many of the predicted structures have yet to be characterized and are absent from traditional chemical databases, but have a higher probability of being present in planta. PlantMAT allows users to operate an automated and streamlined workflow for metabolite annotation from a user-friendly interface within Microsoft Excel, a familiar, easily accessed program for chemists and biologists. The usefulness of PlantMAT is exemplified using ultrahigh-performance liquid chromatography-electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC-ESI-QTOF-MS/MS) metabolite profiling data of saponins and glycosylated flavonoids from the model legume Medicago truncatula. The results demonstrate PlantMAT substantially increases the chemical/metabolic space of traditional chemical databases. Ten of the PlantMAT-predicted identifications were validated and confirmed through the isolation of the compounds using ultrahigh-performance liquid chromatography-mass spectrometry-solid-phase extraction (UHPLC-MS-SPE) followed by de novo structural elucidation using 1D/2D nuclear magnetic resonance (NMR). It is further demonstrated that PlantMAT enables the dereplication of previously identified metabolites and is also a powerful tool for the discovery of structurally novel metabolites.

Pathway-specific metabolome analysis with 18O2-labeled Medicago truncatula via a mass spectrometry-based approach.

INTRODUCTION: Oxygen from carbon dioxide, water or molecular oxygen, depending on the responsible enzyme, can lead to a large variety of metabolites through chemical modification. OBJECTIVES: Pathway-specific labeling using isotopic molecular oxygen (18O2) makes it possible to determine the origin of oxygen atoms in metabolites and the presence of biosynthetic enzymes (e.g., oxygenases). In this study, we established the basis of 18O2-metabolome analysis. METHODS: 18O2 labeled whole Medicago truncatula seedlings were prepared using 18O2-air and an economical sealed-glass bottle system. Metabolites were analyzed using high-accuracy and high-resolution mass spectrometry. Identification of the metabolite was confirmed by NMR following UHPLC-solid-phase extraction (SPE). RESULTS: A total of 511 peaks labeled by 18O2 from shoot and 343 peaks from root were annotated by untargeted metabolome analysis. Additionally, we identified a new flavonoid, apigenin 4'-O-[2'-O-coumaroyl-glucuronopyranosyl-(1-2)-O-glucuronopyranoside], that was labeled by 18O2. To the best of our knowledge, this is the first report of apigenin 4'-glucuronide in M. truncatula. Using MSn analysis, we estimated that 18O atoms were specifically incorporated in apigenin, the coumaroyl group, and glucuronic acid. For apigenin, an 18O atom was incorporated in the 4'-hydroxy group. Thus, non-specific incorporation of an 18O atom by recycling during one month of labeling is unlikely compared with the more specific oxygenase-catalyzing reaction. CONCLUSION: Our finding indicated that 18O2 labeling was effective not only for the mining of unknown metabolites which were biosynthesized by oxygenase-related pathway but also for the identification of metabolites whose oxygen atoms were derived from oxygenase activity.

Quantitation of estrogens in ground water and swine lagoon samples using solid-phase extraction, pentafluorobenzyl/trimethylsilyl derivatizations and gas chromatography-negative ion chemical ionization tandem mass spectrometry.

A method was developed for the confirmed identification and quantitation of 17beta-estradiol, estrone, 17alpha-ethynylestradiol and 16alpha-hydroxy-17beta-estradiol (estriol) in ground water and swine lagoon samples. Centrifuged and filtered samples were extracted using solid-phase extraction (SPE), and extracts were derivatized using pentafluorobenzy] bromide (PFBBR) and N-trimethylsilylimidazole (TMSI). Analysis was done using negative ion chemical ionization (NICI) gas chromatography-mass spectrometry-mass spectrometry (GC-MS-MS). Deuterated analogs of each of the estrogens were used as isotope dilution standards (IDS) and were added to the samples before extraction. A limit of quantitation of 1 ng/l in ground water was obtained using 500 ml of ground water sample, 1.0 ml of extract volume and the lowest calibration standard of 0.5 pg/microl. For a 25 ml swine lagoon sample, the limit of quantitation was 40 ng/l. The average recovery of the four estrogens spiked into 500 ml of distilled water and ground water samples (n = 16) at 2 ng/l was 103% (S.D. 14%). For 25 ml of swine lagoon samples spiked at 500, 1000 and 10,000 ng/l, the average recovery for the four estrogens was 103% (S.D. 15%). The method detection limits (MDLs) of the four estrogens spiked at 2 ng/l in a 500 ml of ground water sample ranged from 0.2 to 0.6 ng/l. In swine lagoon samples from three different types of swine operations, estrone was found at levels up to 25,000 ng/l, followed by estriol and estradiol up to levels at 10,000 and 3000 ng/l, respectively. It was found that pretreatment of swine lagoon samples with formaldehyde was necessary to prevent conversion of estradiol to estrone.

Bromination of aromatic compounds by residual bromide in sodium chloride matrix modifier salt during heated headspace GC/MS analysis.

Analytical artifacts attributed to the bromination of toluene, xylenes, and trimethylbenzenes were found during the heated headspace gas chromatography/mass spectrometry (GC/MS) analysis of aqueous samples. The aqueous samples were produced from Fenton-like chemical oxidation reactions and contained aromatic compounds, hydrogen peroxide (H2O2), and ferric sulfate. Prior to GC/MS headspace analysis, the samples were acidified (pH<2), and sodium chloride was amended to the headspace vial as a matrix modifier. The brominated artifacts were generated during heated headspace analysis. Further, when samples were spiked with a mixture of volatile chlorinated and aromatic compounds (50 µg/L), poor spike recoveries of toluene and xylenes occurred, and in some cases complete loss of trimethylbenzenes and naphthalene resulted. Where poor recovery of aromatic spike compounds occurred, brominated aromatic compounds were found. The only significant source of bromine in the reaction scheme is the bromide typically present (<0.01% w/w) in the sodium chloride amended to the samples. Conversely, brominated artifacts were absent when a buffered salt mixture composed of sodium chloride and potassium phosphate dibasic/monobasic was used as a matrix modifier and raised the sample pH (pH~6). This indicated that the brominated artifacts resulted from the reaction of the aromatic compounds with BrCl, which was formed by the reaction of H2O2, chloride, and bromide under acidic conditions. An alternative matrix modifier salt is recommended that prevents the bromination reaction and avoids these deleterious effects on sample integrity during headspace analysis.

Perchlorate behavior in a municipal lake following fireworks displays.

Perchlorate salts of potassium and ammonium are the primary oxidants in pyrotechnic mixtures, yet insufficient information is available regarding the relationship between fireworks displays and the environmental occurrence of perchlorate. Here we document changes in perchlorate concentrations in surface water adjacent to a site of fireworks displays from 2004 to 2006. Preceding fireworks displays, perchlorate concentrations in surface water ranged from 0.005 to 0.081 microg/L, with a mean value of 0.043 microg/L. Within 14 h after the fireworks, perchlorate concentrations spiked to values ranging from 24 to 1028x the mean baseline value. A maximum perchlorate concentration of 44.2 microg/L was determined following the July 4th event in 2006. After the fireworks displays, perchlorate concentrations decreased toward the background level within 20 to 80 days, with the rate of attenuation correlating to surface water temperature. Adsorption tests indicate that sediments underlying the water column have limited (< 100 nmol/g) capacity to remove perchlorate via chemical adsorption. Microcosms showed comparatively rapid intrinsic perchlorate degradation in the absence of nitrate consistent with the observed disappearance of perchlorate from the study site. This suggests that at sites with appropriate biogeochemical conditions, natural attenuation may be an important factor affecting the fate of perchlorate following fireworks displays.

Analysis of lagoon samples from different concentrated animal feeding operations for estrogens and estrogen conjugates.

Although Concentrated Animal Feeding Operations (CAFOs) have been identified as potentially important sources for the release of estrogens into the environment, information is lacking on the concentrations of estrogens in whole lagoon effluents (including suspended solids) which are used for land application. Lagoons associated with swine, poultry, and cattle operations were sampled at three locations each for direct analysis for estrogens by GC/ MS/MS and estrogen conjugates by LC/MS/MS. Estrogen conjugates were also analyzed indirectly by first subjecting the same samples to enzyme hydrolysis. Solids from centrifuged samples were extracted for free estrogens to estimate total estrogen load. Total free estrogen levels (estrone, 17alpha-estradiol, 17beta-estradiol, estriol) were generally higher in swine primary (1000-21000 ng/L), followed by poultry primary (1800-4000 ng/L), dairy secondary (370-550 ng/L), and beef secondary (22-24 ng/L) whole lagoon samples. Swine and poultry lagoons contained levels of 17(alpha-estradiol comparable to those of 17beta-estradiol. Confirmed estrogen conjugates included estrone-3-sulfate (2-91 ng/L), 17beta-estradiol-3-sulfate (8-44 ng/L), 17alpha-estradiol-3-sulfate (141-182 ng/L), and 17beta-estradiol-17-sulfate (72-84 ng/L) in some lagoons. Enzymatic hydrolysis indicated the presence of additional unidentified estrogen conjugates not detected bythe LC/MS/MS method. In most cases estrogen conjugates accounted for at least a third of the total estrogen equivalents. Collectively, these methods can be used to better determine estrogen loads from CAFO operations, and this research shows that estrogen conjugates contribute significantly to the overall estrogen load, even in different types of CAFO lagoons.

Avoiding hydrolysis of fuel ether oxygenates during static headspace analysis.

The determination of fuel ether oxygenates in groundwater was found to be problematic when samples are preserved at pH < 2 and then analyzed using heated headspace sampling. Acid catalyzed the hydrolysis of tert-amyl methyl ether, ethyl tert-butyl ether, and methyl tert-butyl ether during headspace sampling when aqueous samples were heated at 80 degrees C, a typical temperature used for heated headspace sampling. Hydrochloric acid at pH 2 did not cause hydrolysis of oxygenate ethers in samples stored for 28 d at 4 degrees C. When trisodium phosphate was used to preserve the sample or to adjust the pH of samples preserved with acid before headspace sampling, the recovery of spiked ethers was excellent. The heated headspace method was also applicable for the determination of other fuel oxygenates including ethanol, tert-butyl alcohol (TBA), tert-amyl alcohol (TAA), isopropyl alcohol (IPA), acetone, and monoaromatic compounds found in gasoline including benzene, toluene, ethylbenzene, xylenes, and trimethylbenzenes. The method detection limits range from 0.1 to 0.2 microg/L for the ethers and aromatics. For alcohols and acetone, the method detection limits were 0.8 microg/L for TBA, 18 microg/L for ethanol, 1.2 microg/L for TAA, 5.5 microg/L for IPA, and 3.3 microg/L for acetone. The heated headspace method yielded accurate results for ether oxygenates in samples containing a wide range of gasoline concentrations (2500-100000 microg/L).