Metabolite profiling by mass spectrometry (MS) is an area of interest for disease diagnostics, biomarker discovery, and therapeutic evaluation. A recently developed approach, multiple reaction monitoring (MRM)-profiling, searches for metabolites with precursor (Prec) and neutral loss (NL) scans in a representative sample and creates a list of ion transitions. These are then used in an MRM method for fast screening of individual samples and discrimination between healthy and diseased. A large variety of functional groups are considered and all signals discovered are recorded in the individual samples, making this a largely unsupervised method. MRM-profiling is described here and then demonstrated with data for over 900 human plasma coronary artery disease (CAD) samples. Representative pooled samples for each condition were interrogated using a library of over a hundred Prec and NL scans on a triple quadrupole MS. The data from the Prec and NL experiments were converted into ion transitions, initially some 1266 transitions. Each ion transition was examined in the individual samples on a time scale of milliseconds per transition, which allows for rapid screening of large sample sets (<5 days for 1000 samples). Use of univariate and multivariate statistics allowed classification of the sample set with high accuracy. The metabolite profiles classified the CAD female, CAD male, and peripheral artery disease (PAD) samples relative to controls with an accuracy of 90%, 78%, and 85%, respectively. The compounds responsible for informative ion transitions were identified by chromatography and high resolution MS; some have been previously reported and found to be associated with coronary artery disease metabolism, indicating that the methodology generates a meaningful metabolite profile while being faster than traditional methodologies.

Malaria is a global infectious disease that threatens the lives of millions of people. Transcriptomics, proteomics and functional genomics studies, as well as sequencing of the Plasmodium falciparum and Homo sapiens genomes, have shed new light on this host-parasite relationship. Recent advances in accurate mass measurement mass spectrometry, sophisticated data analysis software, and availability of biological pathway databases, have converged to facilitate our global, untargeted biochemical profiling study of in vitro P. falciparum-infected (IRBC) and uninfected (NRBC) erythrocytes. In order to expand the number of detectable metabolites, several key analytical steps in our workflows were optimized. Untargeted and targeted data mining resulted in detection of over one thousand features or chemical entities. Untargeted features were annotated via matching to the METLIN metabolite database. For targeted data mining, we queried the data using a compound database derived from a metabolic reconstruction of the P. falciparum genome. In total, over one hundred and fifty differential annotated metabolites were observed. To corroborate the representation of known biochemical pathways from our data, an inferential pathway analysis strategy was used to map annotated metabolites onto the BioCyc pathway collection. This hypothesis-generating approach resulted in over-representation of many metabolites onto several IRBC pathways, most prominently glycolysis. In addition, components of the "branched" TCA cycle, partial urea cycle, and nucleotide, amino acid, chorismate, sphingolipid and fatty acid metabolism were found to be altered in IRBCs. Interestingly, we detected and confirmed elevated levels for cyclic ADP ribose and phosphoribosyl AMP in IRBCs, a novel observation. These metabolites may play a role in regulating the release of intracellular Ca2+ during P. falciparum infection. Our results support a strategy of global metabolite profiling by untargeted data acquisition. Untargeted and targeted data mining workflows, when used together to perform pathway-inferred metabolomics, have the benefit of obviating MS/MS confirmation for every detected compound.

Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn2+ before induction, the post‐translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo‐enzyme was prepared and reconstituted with two equivalents of FeSO4. Inductively coupled plasma mass spectrometry and Mössbauer spectroscopy demonstrated that this protein contained two high‐spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [FeII/FeII]‐ADE catalyzed the conversion of H2O2 to O2 and H2O. The values of kcat and kcat/Km for the catalase activity are 200 s−1 and 2.4 × 104 M−1 s−1, respectively. [FeII/FeII]‐ADE underwent more than 100 turnovers with H2O2 before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high‐spin ferric with gave = 4.3 EPR signal and no evidence of anti‐ferromagnetic spin‐coupling. A model is proposed for the disproportionation of H2O2 by [FeII/FeII]‐ADE that involves the cycling of the binuclear metal center between the di‐ferric and di‐ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.

A successful metabolonnics study requires a workflow strategy that can unravel the complexity of the data and reveal the real changes that occur in the system. A workflow that combines untargeted (discovery) quadrupole time-of-flight (Q-TOF) liquid chromatography mass spectrometry (LC-MS), targeted (confirmation) triple-quadrupole LC-MS-MS, and sophisticated data mining is an effective means to elucidate metabolite changes.

Limonoids are considered as potential cancer chemopreventive agents and are widely distributed in the Citrus genus as aglycones and glucosides. In the present study, reversed-phase HPLC coupled with CID mass spectra was developed for the simultaneous separation and identification of aglycones and glucosides of limonoids from citrus. Five aglycones such as limonin, deacetyl nomilin, ichangin, isolimonoic acid and nomilin were identified by positive ion CID MS/MS, whereas five glucosides, viz. limonin glucoside, isoobacunoic acid glucoside, obacunone glucoside, deacetyl nomilinic acid glucoside and nomilinic acid glucoside were analyzed by negative ion CID mass spectra. The developed method was successfully applied to complex citrus samples for the separation and identification of aglycones and glucosides. Citrus seeds were extracted with methanol and partially purified and analyzed by LC-CID mass spectra. The separation was achieved by C-18 column; eight limonoids were identified by comparing the retention times and mass spectral fragmentation. To the best of our knowledge, this is the first report on the identification of citrus limonoids using CID technique.

The 10 fatty acid ester components of brood pheromone were extracted from larvae of different populations of USA and South African honey bees and subjected to gas chromatography-mass spectrometry quantitative analysis. Extractable amounts of brood pheromone were not significantly different by larval population; however, differences in the proportions of components enabled us to classify larval population of 77% of samples correctly by discriminant analysis. Honeybee releaser and primer pheromone responses to USA,Africanized and–European pheromone blends were tested. Texas-Africanized and Georgia-European colonies responded with a significantly greater ratio of returning pollen foragers when treated with a blend from the same population than from a different population. There was a significant interaction of pheromone blend by adult population source among Georgia-European bees for modulation of sucrose response threshold, a primer response. Brood pheromone blend variation interacted with population for pollen foraging response of colonies, suggesting a self recognition cue for this pheromone releaser behavior. An interaction of pheromone blend and population for priming sucrose response thresholds among workers within the first week of adult life suggested a more complex interplay of genotype, ontogeny, and pheromone blend.

Fruits of Citrus aurantifolia were subjected to hydro-distillation using Clevenger type apparatus to obtain volatile oil. Chemical composition of volatile oil was analysed by GC–MS. Twenty-two compounds representing more than 89.5% of the volatile oil were identified. d-limonene (30.13%) and d-dihydrocarvone (30.47%) were found to be the major compounds in the lime volatile oil. This oil showed 78% inhibition of human colon cancer cells (SW-480) with 100 μg/ml concentration at 48 h. Lime volatile oil showed DNA fragmentation and induction of caspase-3 up to 1.8 and 2- folds after 24 h and 48 h, respectively, which may be due to the involvement of apoptosis. Analysis of apoptosis-related protein expression further confirmed apoptosis induction by lime volatile oil. The above results suggested that lime volatile oil has potential benefits in colon cancer prevention. This is the first report, showing the possible mechanism of antiproliferative effect of lime volatile oil for the prevention of colon cancer in cell culture models.

The gas-phase H/D exchange reactions of arginine (R) and arginine-containing di- and tri-peptide (gly-arg (GR), arg-gly (RG), gly-gly-arg (GGR), gly-arg-gly (GRG) and arg-gly-gly (RGG)) [M + H]+ ions with deuterated ammonia (ND3) were investigated by using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR), ion mobility-mass spectrometry (IM-MS), ab initio and density functional theory-based molecular orbital calculations and molecular modeling. Three exchanges are observed for arginine and arginine-containing tri-peptide [M + H]+ ions, whereas the di-peptide [M + H]+ ions undergo a single H/D exchange. In addition, C-terminal methylation blocks H/D exchange of arginine and the arginine-containing peptide [M + H]+ ions, and a single H/D exchange is observed for N-terminal acetylated arginine [M + H]+ ions. A general mechanism for H/D exchange involving a collision complex that is best described as a "solvated salt-bridge" structure is proposed.

The high-temperature requirement A (HtrA) family of serine proteases has been shown to play an important role in the environmental and cellular stress damage control system in Escherichia coli. Mycobacterium tuberculosis ( Mtb) has three putative HtrA-like proteases, HtrA1, HtrA2, and HtrA3. The deletion of htrA2 gives attenuated virulence in a mouse model of TB. Biochemical analysis reveals that HtrA2 can function both as a protease and as a chaperone. The three-dimensional structure of HtrA2 determined at 2.0 A resolution shows that the protease domains form the central core of the trimer and the PDZ domains extend to the periphery. Unlike E. coli DegS and DegP, the protease is naturally active due to the formation of the serine protease-like catalytic triad and its uniquely designed oxyanion hole. Both protease and PDZ binding pockets of each HtrA2 molecule are occupied by autoproteolytic peptide products and reveal clues for a novel autoregulatory mechanism that might have significant importance in HtrA-associated virulence of Mtb.

Although sterol carrier protein-2 (SCP-2) is encoded as a precursor protein (proSCP-2), little is known regarding the structure and function of the 20-amino acid N-terminal presequence. As shown herein, the presequence contains significant secondary structure and alters SCP-2: (i) secondary structure (CD), (ii) tertiary structure (aqueous exposure of Trp shown by UV absorbance, fluorescence, and fluorescence quenching), (iii) ligand binding site [Trp response to ligands, peptide cross-linked by photoactivatable free cholesterol (FCBP)], (iv) selectivity for interaction with anionic phospholipid-rich membranes, (v) interaction with a peroxisomal import protein [FRET studies of Pex5p(C) binding], the N-terminal presequence increased SCP-2's affinity for Pex5p(C) by 10-fold, and (vi) intracellular targeting in living and fixed cells (confocal microscopy). Nearly 5-fold more SCP-2 than proSCP-2 colocalized with plasma membrane lipid rafts and caveolae (AF488-CTB); 2.8-fold more SCP-2 than proSCP-2 colocalized with a mitochondrial marker (Mitotracker), but nearly 2-fold less SCP-2 than proSCP-2 colocalized with peroxisomes (AF488 antibody to PMP70). These data indicate the importance of the N-terminal presequence in regulating SCP-2 structure, cholesterol localization within the ligand binding site, membrane association, and, potentially, intracellular targeting.

An unusual class of diterpenoid natural products, 'cycloterpenals' (with a central cyclohexadienal core), that arise in nature by condensation of retinoids and other isoprenes, have been isolated from a variety of organisms including marine sponges as well as from the human eye. A milk whey protein has also demonstrated the formation of a cycloterpenal derived from beta-ionylidineacetaldehyde. Here, we generate a synthetic library of these molecules where we detail reaction conditions required to effect cross condensation of alpha,beta-unsaturated aldehydes as opposed to homodimerization. The ability of this class of molecules to activate neurite outgrowth activity is reported.

An ion mobility-mass spectrometer (IM-MS) interface is described that can be employed to perform collisional activation and/or collision-induced dissociation (CID) with good transmission of mobility separated ions to the MS analyzer. The IM-MS interface consists of a stacked-ring ion guide design, where the field strength and pressure ratio can be operated such that structural rearrangement reactions and/or CID are achieved as a function of the effective ion temperature. The ion dynamics and collisional activation processes in the IM-MS interface are described as a function of the ion-neutral collisions, ion kinetic energies, and effective ion temperature. The applicability of the IM-CID-MS methodology to studies of peptide ion fragmentation is illustrated using a series of model peptides.

The blackbody infrared radiation induced dissociation of methyl benzoate (C8H8O2(+*)) radical cation was investigated by using a Fourier transfer ion cyclotron resonance mass spectrometer equipped with a resistively heated (wire temperatures of 400-1070 K) wire ion guide. We observed product ion branching ratios that are strongly dependent upon wire temperature. At low temperatures (670-890 K) the major product ion C7H8 (+*) (m/z 92), which is formed by loss of CO2, and at higher temperatures (above 900 K), loss of methoxy radical ((*)OCH3) competes with loss of CO2. The energies of the various reactant ions and transition states for product ion formation were estimated by using density functional theory molecular orbital calculations, and a proposed mechanism for the dissociation chemistry of C8H8O2 (+*) involving a multistep rearrangement reaction is tested using the Master Equation formalism.

The purpose of this study is to determine whether the nature of the post-translational modifications of the major apolipoproteins of HDL is different for density-distinct subclasses. These subclasses were separated by ultracentrifugation using a novel density-forming solute to yield a high-resolution separation. The serum of two subjects, a control with a normolipidemic profile and a subject with diagnosed cardiovascular disease, was studied. Aliquots of three HDL subclasses were analyzed by MALDI and considerable differences were seen when comparing density-distinct subclasses and also when comparing the two subjects. A detailed analysis of the post-translational modification pattern of apoA-1 shows evidence of considerable protease activity, particularly in the more dense fractions. We conclude that part of the heterogeneity of the population of HDL particles is due to density-dependent protease activity.

A series of porous TiO2–SiO2 mixed metal oxides were synthesized via sol–gel route using n-alkyl amine as pore directing templates. The mixed oxides were characterized by nitrogen physisorption for surface area, pore volume and pore size distribution, as well as by FTIR, TGA, SEM, and TEM for the dispersion of titanium. These compounds are good catalysts for liquid phase epoxidation of cyclohexene using hydrogen peroxide as the oxidant. The effects of various factors on catalyst reactivity were also studied. The catalysts performance and selectivity are enhanced in protic solvents when compared to aprotic solvents.

Dichlorocarbene radical cation reacts with benzaldehyde in the gas phase by oxygen radical anion abstraction, generating a new carbene radical cation population. The ion population consists of two isomeric carbene radical cations. Molecular orbital calculations, diagnostic ion-molecule reactions, and examination of ion-molecule reactions’ kinetics and thermochemistry were utilized to elucidate the structures (phenylcarbene radical cation and dehydrotropylium cation), provide the relative abundances (20% and 80%, respectively) and propose a likely mechanism for the formation of the two isomeric carbene radical cations. A single potential energy surface was found to explain the formation of both carbene radical cations. Oxygen radical anion abstraction followed by prompt dissociation of the collision complex leads to the formation of the phenylcarbene radical cation. However, in a longer-lived collision complex, the phenylcarbene radical cation can rearrange to a more stable isomer, the dehydrotropylium cation.