PubMed

Investigation of the effect of genotype and agronomic conditions on metabolomic profiles of selected strawberry cultivars with different sensitivity to environmental stress. Plant Physiol Biochem. 2016 Jan 22;101:14-22 Authors: Akhatou I, González-Domínguez R, Fernández-Recamales Á Abstract Strawberry is one of the most economically important and widely cultivated fruit crops across the world, so that there is a growing need to develop new analytical methodologies for the authentication of variety and origin, as well as the assessment of agricultural and processing practices. In this work, an untargeted metabolomic strategy based on gas chromatography mass spectrometry (GC-MS) combined with multivariate statistical techniques was used for the first time to characterize the primary metabolome of different strawberry cultivars and to study metabolite alterations in response to multiple agronomic conditions. For this purpose, we investigated three varieties of strawberries with different sensitivity to environmental stress (Camarosa, Festival and Palomar), cultivated in soilless systems using various electrical conductivities, types of coverage and substrates. Metabolomic analysis revealed significant alterations in primary metabolites between the three strawberry cultivars grown under different crop conditions, including sugars (fructose, glucose), organic acids (malic acid, citric acid) and amino acids (alanine, threonine, aspartic acid), among others. Therefore, it could be concluded that GC-MS based metabolomics is a suitable tool to differentiate strawberry cultivars and characterize metabolomic changes associated with environmental and agronomic conditions. PMID: 26841267 [PubMed - as supplied by publisher]

Fragmentation trees reloaded. J Cheminform. 2016;8:5 Authors: Böcker S, Dührkop K Abstract BACKGROUND: Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds. One of the bottlenecks in this experimental setup is the interpretation of fragmentation spectra to accurately and efficiently identify compounds. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are determined from the data using combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. Fragmentation tree computation does not require spectral or structural databases. To obtain biochemically meaningful trees, one needs an elaborate optimization function (scoring). RESULTS: We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our method SIRIUS 3, performs significantly better than the previous version of our method, as well as other methods for this task. CONCLUSION: SIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing researchers to investigate unknowns using automated computational methods.Graphical abstractWe present a new scoring for computing fragmentation trees from tandem mass spectrometry data based on Bayesian statistics. The best scoring fragmentation tree most likely explains the molecular formula of the measured parent ion. PMID: 26839597 [PubMed]

Influence of the collection tube on metabolomic changes in serum and plasma. Talanta. 2016 Apr 1;150:681-9 Authors: López-Bascón MA, Priego-Capote F, Peralbo-Molina A, Calderón-Santiago M, Luque de Castro MD Abstract Major threats in metabolomics clinical research are biases in sampling and preparation of biological samples. Bias in sample collection is a frequently forgotten aspect responsible for uncontrolled errors in metabolomics analysis. There is a great diversity of blood collection tubes for sampling serum or plasma, which are widely used in metabolomics analysis. Most of the existing studies dealing with the influence of blood collection on metabolomics analysis have been restricted to comparison between plasma and serum. However, polymeric gel tubes, which are frequently proposed to accelerate the separation of serum and plasma, have not been studied. In the present research, samples of serum or plasma collected in polymeric gel tubes were compared with those taken in conventional tubes from a metabolomics perspective using an untargeted GC-TOF/MS approach. The main differences between serum and plasma collected in conventional tubes affected to critical pathways such as the citric acid cycle, metabolism of amino acids, fructose and mannose metabolism and that of glycerolipids, and pentose and glucuronate interconversion. On the other hand, the polymeric gel only promoted differences at the metabolite level in serum since no critical differences were observed between plasma collected with EDTA tubes and polymeric gel tubes. Thus, the main changes were attributable to serum collected in gel and affected to the metabolism of amino acids such as alanine, proline and threonine, the glycerolipids metabolism, and two primary metabolites such as aconitic acid and lactic acid. Therefore, these metabolite changes should be taken into account in planning an experimental protocol for metabolomics analysis. PMID: 26838459 [PubMed - in process]

Direct and simultaneous quantification of ATP, ADP and AMP by (1)H and (31)P Nuclear Magnetic Resonance spectroscopy. Talanta. 2016 Apr 1;150:485-92 Authors: Lian Y, Jiang H, Feng J, Wang X, Hou X, Deng P Abstract ATP, ADP and AMP are energy substances with vital biological significance. Based on the structural differences, a simple, rapid and comprehensive method has been established by (1)H and (31)P Nuclear Magnetic Resonance ((1)H-NMR and (31)P-NMR) spectroscopies. Sodium 3-(trimethylsilyl) propionate-2,2,3,3-d4 (TMSP) and anhydrous disodium hydrogen phosphate (Na2HPO4) were selected as internal standards for (1)H-NMR and (31)P-NMR, respectively. Those three compounds and corresponding internal standards can be easily distinguished both by (1)H-NMR and (31)P-NMR. In addition, they all have perfect linearity in a certain range: 0.1-100mM for (1)H-NMR and 1-75mM for (31)P-NMR. To validate the precision of this method, mixed samples of different concentrations were measured. Recovery experiments were conducted in serum (91-113% by (1)H-NMR and 89-113% by (31)P-NMR). PMID: 26838434 [PubMed - in process]

Evaluating the potential of LC coupled to three alternative detection systems (ESI-IT, APCI-TOF and DAD) for the targeted determination of triterpenic acids and dialcohols in olive tissues. Talanta. 2016 Apr 1;150:355-66 Authors: Olmo-García L, Bajoub A, Fernández-Gutiérrez A, Carrasco-Pancorbo A Abstract Herewith the development of a rapid and powerful LC methodology (with three different detectors) is presented to determine triterpenic acids and dialcohols in extracts from Olea europaea tissues (olive skin, pulp and leaves). After the proper optimization of the LC, DAD and MS conditions and the comprehensive characterization of the behavior of each analyte in ESI and APCI (with accurate m/z signals and, in ESI, with MS/MS data too), the method was fully validated. DAD, ESI-IT MS and APCI-QTOF MS were used as detection systems to give different alternatives to carry out the accurate determination of these analytes, evaluate their analytical performance, advantages and drawbacks, and check whether the quantitative results achieved by the three platforms were in good agreement. ESI-IT MS gave the lowest detection limits (3-455μg/L) followed by APCI-QTOF MS (22-408μg/L); in contrast, DAD (83-600μg/L) had the widest dynamic range. The RSD values for inter-day repeatability were found below 11.82% in all the cases. No statistically significant differences were found among the quantitative results from the three detectors. Olive leaves showed the highest concentration levels of ursolic acid (1.8mg/g), erythrodiol (1.6mg/g) and uvaol (1.2mg/g), whereas the olive skin was the richest matrix in terms of maslinic (80mg/g), betulinic (0.20mg/g), and oleanolic (26mg/g) acids. Concentration values of triterpenic acids were established by first time for skinless olive pulp, and were found around 65, 1.2, 55 and 4.4μg/g for maslinic, betulinic, oleanolic and ursolic acids, respectively. PMID: 26838419 [PubMed - in process]

Bar Coding MS(2) Spectra for Metabolite Identification. Anal Chem. 2016 Feb 2; Authors: Spalding JL, Cho K, Mahieu NG, Nikolskiy I, Llufrio EM, Johnson SL, Patti GJ Abstract Metabolite identifications are most frequently achieved in untargeted metabolomics by matching precursor mass and full, high-resolution MS(2) spectra to metabolite databases and standards. Here we considered an alternative approach for establishing metabolite identifications that does not rely on full, high-resolution MS(2) spectra. First, we select mass-to-charge regions containing the most informative metabolite fragments and designate them as bins. We then translate each metabolite fragmentation pattern into a binary code by assigning 1's to bins containing fragments and 0's to bins without fragments. With 20 bins, this binary-code system is capable of distinguishing 96% of the compounds in the METLIN MS(2) library. A major advantage of the approach is that it extends untargeted metabolomics to low-resolution triple quadrupole (QqQ) instruments, which are typically less expensive and more robust than other types of mass spectrometers. We demonstrate a method of acquiring MS(2) data in which the third quadrupole of a QqQ instrument cycles over 20 wide isolation windows (coinciding with the location and width of our bins) for each precursor mass selected by the first quadrupole. Operating the QqQ instrument in this mode yields diagnostic bar codes for each precursor mass that can be matched to the bar codes of metabolite standards. Furthermore, our data suggest that using low-resolution bar codes enables QqQ instruments to make MS(2)-based identifications in untargeted metabolomics with a specificity and sensitivity that is competitive to high-resolution time-of-flight technologies. PMID: 26837423 [PubMed - as supplied by publisher]

Related Articles Effects of cyclin-dependent kinase inhibitor Purvalanol B application on protein expression and developmental progression in intra-erythrocytic Plasmodium falciparum parasites. Malar J. 2015;14:147 Authors: Bullard KM, Broccardo C, Keenan SM Abstract BACKGROUND: The 2013 Malaria World Report indicated that in 2012 there were approximately 207 million cases of malaria, which resulted in an estimated 627,000 malaria-related deaths. Due to the alarming resistance of these parasites to traditional anti-malarial treatments there is a pressing need to not only identify new anti-malarial compounds, but also to characterize the effect of compounds known to have an effect on the parasite life cycle. This study reports on effects of kinase inhibitor Purvalanol B administration on the growth and protein expression of Plasmodium falciparum late-stage trophozoites. METHODS: A SYBR® Green I parasite growth assay was used to measure the IC50 of Purvalanol B with P. falciparum (strain W2). Purvalanol B or DMSO control were applied to synchronized parasites 36 hours post invasion and parasites were incubated for 12 hours. Giemsa-stained blood smears were used to determine the effect of Purvalanol B on parasite growth, global quantitative proteomic analysis was used to examine differences in protein expression between Purvalanol B-treated and control parasites and results were confirmed by qPCR. RESULTS: There were no differences in parasitaemia between inhibitor-treated and control parasites. However, the ability of Purvalanol B-treated parasites to form schizonts was significantly reduced. Proteomic analysis detected 76 human proteins and 518 P. falciparum proteins (63 in control cultures only, 56 proteins in Purvalanol B cultures only, and 399 proteins in both cultures). Quantitative analysis of protein extracts revealed eight proteins that were up-regulated in the inhibitor-treated cultures, including several components of the parasite's proteasome complex and thioredoxin reductase. Two proteins appeared to be down-regulated, including a helicase and an RNA-binding protein. CONCLUSION: Purvalanol B application decreases the ability of late-stage P. falciparum trophozoites to form multinucleated schizonts and up-regulates proteasome subunits and proteins that contribute to redox homeostasis, which may indicate an increase in oxidative stress as a result of inhibitor application. While the efficacy of Purvalanol B is relatively low for use as an anti-malarial therapy, quantitative proteomic analysis may serve as a method of examining the action of drugs on the parasite and indicate the likelihood of future resistance development. PMID: 25879664 [PubMed - indexed for MEDLINE]

Related Articles Hinge-Region O-Glycosylation of Human Immunoglobulin G3 (IgG3). Mol Cell Proteomics. 2015 May;14(5):1373-84 Authors: Plomp R, Dekkers G, Rombouts Y, Visser R, Koeleman CA, Kammeijer GS, Jansen BC, Rispens T, Hensbergen PJ, Vidarsson G, Wuhrer M Abstract Immunoglobulin G (IgG) is one of the most abundant proteins present in human serum and a fundamental component of the immune system. IgG3 represents ∼8% of the total amount of IgG in human serum and stands out from the other IgG subclasses because of its elongated hinge region and enhanced effector functions. This study reports partial O-glycosylation of the IgG3 hinge region, observed with nanoLC-ESI-IT-MS(/MS) analysis after proteolytic digestion. The repeat regions within the IgG3 hinge were found to be in part O-glycosylated at the threonine in the triple repeat motif. Non-, mono- and disialylated core 1-type O-glycans were detected in various IgG3 samples, both poly- and monoclonal. NanoLC-ESI-IT-MS/MS with electron transfer dissociation fragmentation and CE-MS/MS with CID fragmentation were used to determine the site of IgG3 O-glycosylation. The O-glycosylation site was further confirmed by the recombinant production of mutant IgG3 in which potential O-glycosylation sites had been knocked out. For IgG3 samples from six donors we found similar O-glycan structures and site occupancies, whereas for the same samples the conserved N-glycosylation of the Fc CH2 domain showed considerable interindividual variation. The occupancy of each of the three O-glycosylation sites was found to be ∼10% in six serum-derived IgG3 samples and ∼13% in two monoclonal IgG3 allotypes. PMID: 25759508 [PubMed - indexed for MEDLINE]

Related Articles Characterization of metabolically quiescent Leishmania parasites in murine lesions using heavy water labeling. PLoS Pathog. 2015 Feb;11(2):e1004683 Authors: Kloehn J, Saunders EC, O'Callaghan S, Dagley MJ, McConville MJ Abstract Information on the growth rate and metabolism of microbial pathogens that cause long-term chronic infections is limited, reflecting the absence of suitable tools for measuring these parameters in vivo. Here, we have measured the replication and physiological state of Leishmania mexicana parasites in murine inflammatory lesions using 2H2O labeling. Infected BALB/c mice were labeled with 2H2O for up to 4 months, and the turnover of parasite DNA, RNA, protein and membrane lipids estimated from the rate of deuterium enrichment in constituent pentose sugars, amino acids, and fatty acids, respectively. We show that the replication rate of parasite stages in these tissues is very slow (doubling time of ~12 days), but remarkably constant throughout lesion development. Lesion parasites also exhibit markedly lower rates of RNA synthesis, protein turnover and membrane lipid synthesis than parasite stages isolated from ex vivo infected macrophages or cultured in vitro, suggesting that formation of lesions induces parasites to enter a semi-quiescent physiological state. Significantly, the determined parasite growth rate accounts for the overall increase in parasite burden indicating that parasite death and turnover of infected host cells in these lesions is minimal. We propose that the Leishmania response to lesion formation is an important adaptive strategy that minimizes macrophage activation, providing a permissive environment that supports progressive expansion of parasite burden. This labeling approach can be used to measure the dynamics of other host-microbe interactions in situ. PMID: 25714830 [PubMed - indexed for MEDLINE]

Related Articles Biosynthesis and analysis of plant oxylipins. Free Radic Res. 2015 May;49(5):565-82 Authors: Griffiths G Abstract The term oxylipin is applied to the generation of oxygenated products of polyunsaturated fatty acids that can arise either through non-enzymatic or enzymatic processes generating a complex array of products, including alcohols, aldehydes, ketones, acids and hydrocarbon gases. The biosynthetic origin of these products has revealed an array of enzymes involved in their formation and more recently a radical pathway. These include lipoxygenases and α-dioxygenase that insert both oxygen atoms in to the acyl chain to initiate the pathways, to specialised P450 monooxygenases that are responsible for their downstream processing. This latter group include enzymes at the branch points such as allene oxide synthase, leading to jasmonate signalling, hydroperoxide lyase, responsible for generating pathogen/pest defensive volatiles and divinyl ether synthases and peroxygenases involved in the formation of antimicrobial compounds. The complexity of the products generated raises significant challenges for their rapid identification and quantification using metabolic screening methods. Here the current developments in oxylipin metabolism are reviewed together with the emerging technologies required to expand this important field of research that underpins advances in plant-pest/pathogen interactions. PMID: 25536417 [PubMed - indexed for MEDLINE]

31 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/02/03PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/02/02PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related Articles Postprandial metabolomics: A pilot mass spectrometry and NMR study of the human plasma metabolome in response to a challenge meal. Anal Chim Acta. 2016 Feb 18;908:121-131 Authors: Karimpour M, Surowiec I, Wu J, Gouveia-Figueira S, Pinto R, Trygg J, Zivkovic AM, Nording ML Abstract The study of postprandial metabolism is relevant for understanding metabolic diseases and characterizing personal responses to diet. We combined three analytical platforms - gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) - to validate a multi-platform approach for characterizing individual variation in the postprandial state. We analyzed the postprandial plasma metabolome by introducing, at three occasions, meal challenges on a usual diet, and 1.5 years later, on a modified background diet. The postprandial response was stable over time and largely independent of the background diet as revealed by all three analytical platforms. Coverage of the metabolome between NMR and GC-MS included more polar metabolites detectable only by NMR and more hydrophobic compounds detected by GC-MS. The variability across three separate testing occasions among the identified metabolites was in the range of 1.1-86% for GC-MS and 0.9-42% for NMR in the fasting state at baseline. For the LC-MS analysis, the coefficients of variation of the detected compounds in the fasting state at baseline were in the range of 2-97% for the positive and 4-69% for the negative mode. Multivariate analysis (MVA) of metabolites detected with GC-MS revealed that for both background diets, levels of postprandial amino acids and sugars increased whereas those of fatty acids decreased at 0.5 h after the meal was consumed, reflecting the expected response to the challenge meal. MVA of NMR data revealed increasing postprandial levels of amino acids and other organic acids together with decreasing levels of acetoacetate and 3-hydroxybutanoic acid, also independent of the background diet. Together these data show that the postprandial response to the same challenge meal was stable even though it was tested 1.5 years apart, and that it was largely independent of background diet. This work demonstrates the efficacy of a multi-platform metabolomics approach followed by multivariate and univariate data analysis for a broad-scale screen of the individual metabolome, particularly for studies using repeated measures to determine dietary response phenotype. PMID: 26826694 [PubMed - as supplied by publisher]

Related Articles Development and validation of a CE-MS method for the targeted assessment of amino acids in urine. Electrophoresis. 2016 Jan 30; Authors: Rodrigues KT, Mekahli D, Tavares MF, Van Schepdael A Abstract A CE-ESI-MS method was developed and validated for the separation and quantitative analysis of amino acids in urine. Experimental parameters related to the CE-MS interface, background electrolyte (BGE) and mass spectrometer (MS) settings were optimized providing a good separation of 27 amino acids, including the isomers L-leucine, L-isoleucine and L-alloisoleucine, in less than 30 min. The sheath liquid was composed by 0.50% formic acid in 60% (v,v) methanol-water delivered at a flow rate of 5 μL/min. The BGE consisted of 0.80 mol/L formic acid at pH 1.96 and 15% methanol. A pH stacking procedure was implemented to enhance sensitivity (a 12.5% NH4OH solution was injected at 0.5 psi/9 s prior to samples injected at 0.6 psi/20 s). The proposed method was validated according to FDA and ICH protocols exhibiting acceptable parameters. Analytical curves presented coefficients of determination from 0.996 to 0.9997 (with large F statistics and low p-values). Limits of detection and quantification ranged from 0.63 to 29 μmol/L and from 1.9 to 86 μmol/L, respectively. Practical repeatability was obtained for all AA with coefficients of variation better than 0.55 %CV (migration time) and 1.7 %CV (peak area ratios; methionine sulfone as internal standard). Recoveries of AA in spiked urine ranged from 92.0 to 123% with few exceptions. Moreover, a successful quantification of amino acids in pooled control and test urine samples, which compose a VUR cohort, was achieved showing the potential applicability of the proposed method for targeted metabolomics studies using CE-ESI-MS with an Ion Trap as mass analyzer. This article is protected by copyright. All rights reserved. PMID: 26826549 [PubMed - as supplied by publisher]

Related Articles Editorial: Managing Strategies for Diverse Diseases: Challenges from Bench to Bedside Translation in Successful Drug Discovery and Development. Curr Pharm Des. 2016;22(5):515-7 Authors: Kamal MA, Greig NH PMID: 26825465 [PubMed - in process]

Related Articles METABOLOMIC-DRIVEN ELUCIDATION OF SERUM DISTURBANCES ASSOCIATED WITH ALZHEIMER´S DISEASE AND MILD COGNITIVE IMPAIRMENT. Curr Alzheimer Res. 2016 Jan 28; Authors: González-Domínguez R, Rupérez FJ, García-Barrera T, Barbas C, Gómez-Ariza JL Abstract Numerous efforts have been made in the last years to discover potential biomarkers of Alzheimer's disease and its progression from mild cognitive impairment, considered as an intermediate phase in the development of Alzheimer's disease from normal aging. However, there is still a considerable lack of understanding about pathological mechanisms underlying to disease. In the present study, serum metabolomics based on ultra-high-performance liquid chromatography-mass spectrometry was applied to investigate metabolic differences between subjects with Alzheimer's disease and mild cognitive impairment, as well as healthy controls. The most important findings can be associated with impaired metabolism of phospholipids and sphingolipids leading to membrane breakdown, wherein the nature of the fatty acids contained in the structure in terms of acyl chain length and degree of unsaturation appears to play a crucial role. Furthermore, several discriminant metabolites were found for the first time in relation to known pathological processes associated with Alzheimer's disease, such as the accumulation of acylcarnitines in relation to mitochondrial dysfunction, decreased levels of oleamide and monoglycerides as a result of defects in endocannabinoid system, or increased serum phenylacetylglutamine, which could reveal alterations in glutamine homeostasis. Therefore, these results represent a suitable approximation to understand the pathogenesis and progression of the disease.  . PMID: 26825096 [PubMed - as supplied by publisher]

Related Articles Urinary Metabolomics Reveals Alterations of Aromatic Amino Acid Metabolism of Alzheimer's Disease in the Transgenic CRND8 Mice. Curr Alzheimer Res. 2016 Jan 28; Authors: Tang Z, Liu L, Li Y, Dong J, Li M, Huang J, Lin S, Cai Z Abstract Alzheimer's disease (AD) is a progressive neurodegenerative disorder, with amyloid plaques accumulation as the key feature involved in its pathology. To date, however, the biochemical changes in AD have not been clearly characterized. Here, we present that urinary metabolomics based on high resolution mass spectrometry was employed for delineation of metabolic alterations in transgenic CRND8 mice. In this noninvasive approach, urinary metabolome reveals the biochemical changes in early onset of this AD mouse model. In virtue of comprehensive metabolite profiling and multivariate statistical analysis, a total of 73 differential metabolites of urine sample sets was identified in 12-week and 18-week transgenic mice compared to wild-type littermates, covering perturbations of aromatic amino acids metabolism, the Krebs cycle and one-carbon metabolism. Of particular interest is that divergent tryptophan metabolism, such as upregulation of serotonin pathway while downregulation of kynurenine pathway, was observed. Meanwhile, the accumulation of both N-acetylvanilalanine and 3-methoxytyrosine indicated aromatic L-amino acid decarboxylase deficiency. And the microbial metabolites derived from aromatic amino acid metabolism and drug-like phase II metabolic response via the glycine conjugation reactions were also highlighted, indicating that genetic modification in mouse brain not only alters genotype but also perturbs the gut microbiome. Together, our study demonstrated that the integrative approach employing mass spectrometry-based metabolomics and a transgenic mouse model for AD may provide new evidence for distinct metabolic signatures. The perturbations of metabolic pathways may have far-reaching implications for early diagnosis and intervention in AD. PMID: 26825095 [PubMed - as supplied by publisher]

Metabolic Effects of the pksCT Gene on Monascus aurantiacus Li As3.4384 Using Gas Chromatography-Time-of-Flight Mass Spectrometry-Based Metabolomics. J Agric Food Chem. 2016 Jan 29; Authors: Huang Z, Zhang S, Xu Y, Li L, Li Y Abstract Monascus spp. have been used for the production of natural pigments and bioactive compounds in China for several centuries. Monascus also can produce the mycotoxin citrinin, restricting its use. Disruption of the pksCT gene in Monascus aurantiacus Li AS3.4384 reduces citrinin production capacity of this strain (Monascus PHDS26) by over 98%. However, it is unclear how other metabolites of M. aurantiacus Li AS3.4384 (the wild-type strain) are affected by the pksCT gene. Here, we used metabolomics analyses to compare red yeast rice (RYR) metabolite profiles of the wild-type strain and Monascus PHDS26 at different stages of solid-state fermentation. Eighteen metabolites forming components within the glycolysis, acetyl-CoA, amino acid, and TCA cycle metabolic processes were found to be altered between the wild-type strain and Monascus PHDS26 at different stages of solid-state fermentation. Thus, these findings provide important insights into the metabolic pathways affected by the pksCT gene in M. aurantiacus. PMID: 26824776 [PubMed - as supplied by publisher]

Reply to letter 16-005. Liver Transpl. 2016 Jan 29; Authors: Lahoz A PMID: 26824515 [PubMed - as supplied by publisher]

Statistical correlations between NMR spectroscopy and direct infusion FT-ICR mass spectrometry aid annotation of unknowns in metabolomics. Anal Chem. 2016 Jan 29; Authors: Hao J, Liebeke M, Sommer U, Viant MR, Bundy JG, Ebbels TM Abstract NMR spectroscopy and mass spectrometry are the two major analytical platforms for metabolomics, and both generate substantial data with hundreds to thousands of observed peaks for a single sample. Many of these are unknown, and peak assignment is generally complex and time-consuming. Statistical correlations between data types have proven useful in expediting this process, for example in prioritizing candidate assignments. However, this approach has not been formally assessed for the comparison of direct-infusion mass spectrometry (DIMS) and NMR data. Here, we present a systematic analysis of a sample set (tissue extracts), and the utility of a simple correlation thresh-old to aid metabolite identification. The correlations were surprisingly successful in linking structurally related signals, with 15 of 26 NMR-detectable metabolites having their highest correlation to a cognate MS ion. However, we found that the distribution of the correlations was highly dependent on the nature of the MS ion, such as the adduct type. This approach should help to alleviate this important bottleneck where both 1D NMR and DIMS datasets have been collected. PMID: 26824414 [PubMed - as supplied by publisher]