The sea lamprey (Petromyzon marinus) is a destructive invasive species in the Great Lakes that contributed to the collapse of native fish populations in the mid-1900s. 3-Trifluoromethyl-4-nitrophenol (TFM) is a selective pesticide that has been applied to sea lamprey infested tributaries of the Great Lakes to kill larvae since the 1960s and has reduced the populations by as much as 90%. However, the metabolism of TFM by sea lamprey and non-target species is not fully illuminated. Elucidation of TFM metabolism is critical for understanding its mode of action and possible environmental impact. Here, we describe the screening, identification, synthesis and structural characterization of TFM metabolites in livers from sea lamprey and three non-target species that differ in their ability to survive TFM exposure. We identified glucuronidation, sulfation, N-acetylation, glutathione conjugation, and aromatic nitro group reduction as potential detoxification mechanisms. Seven metabolites were synthesized for use as markers of TFM metabolism in fish. Quantitative 1H NMR was used to assay synthesized metabolite stock solutions that were then used as standard material to develop a quantitative LC-MS/MS method for TFM metabolites.

The sea lamprey (Petromyzon marinus) is a destructive invasive species in the Great Lakes. Since the 1960s, tons of the lampricide 3-trifluoromethyl-4-nitrophenol (TFM) has been applied to selected tributaries each year to eliminate or reduce sea lamprey larval populations. Therefore, the environmental impact of TFM needs to be evaluated. However, the metabolism of TFM and its mechanism of selective toxicity in sea lamprey is not yet fully understood. Based upon our previous report on the identification, synthesis, and characterization of TFM metabolites observed in liver incubates from sea lamprey and non-target fishes, we now provide a robust assay for quantifying TFM and its metabolites in fish liver tissue. This method is important for assessing bioaccumulation of TFM in the ecosystems. The compounds purified in our previous report were used to develop and validate a quantitative ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) assay for TFM and TFM metabolites formed in vivo. Several sample preparation techniques were compared, and a protein precipitation method was selected. The unavailability of stable isotopic internal standards was overcome by using a matrix matching method. After a thorough validation, this method was applied to determine the concentrations of TFM and its metabolites in fish liver tissues from animals exposed to TFM, and in the comparison between dead animals and survivors. Seven of eight expected metabolites were observed, some for the first time in vivo. Our results indicate that in vivo nitroreduction, glucuronidation, sulfation, and glutathione conjugation are involved in TFM metabolism in sea lamprey.

Triacylglycerides (TAGs) are high energy density lipids with a $25 billion commodity at international level. Plant TAGs are produced via a series of chemical reactions catalyzed by certain enzymes including diacylglycerol acyltransferases (DGATs) and phospholipid diacylglycerol acyltransferases (PDATs). In Arabidopsis, certain transcription factors including Wrinkled 1 (Wri1) and Leafy Cotyledons2 (LEC2) supply the necessary substrates for synthesis of fatty acids and/or for packaging of the oil bodies. TAGs will be stored as oil body structurs which certain proteins such as oleosin can protect them from Enzymatic degradation.In this Study, we overexpressed three major genes involved in the TAG biosynthesis and accumulation; 1) dgat1 as a key enzyme in TAGs biosynthesis, 2) wri1 which is the major transcription factor involved in supplies of fatty acids for TAG biosynthesis, and 3) oleosin (Ole) gene which encodes for protein that protects TAGs from degradation. All three genes were integrated in maize genome under a constitutive promoter to allow the production of oil bodies and seed storage oil-like TAG in maize vegetative biomass.Our results indicated an increase in the total leaf oil contents by 79% in the metabolically engineered line. GC-MS analysis detected a total of 13 fatty acids in the leaf oil extract samples, representing ∼99.99% of the total fatty acids. Overall, the percentage of the leaf total saturated (SFA) were decreased while the percentage of monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA) were increased in metabolically engineered plant leaves.This is the first report of increasing TAG accumulation in maize vegetative biomass (stover) via metabolic engineering, which will open new dimension for creating new opportunities to complement and expedite the cellulosic biofuels applications.

Given limited global food supplies and the fact that the global population is expected to double by 2050, there is an urgent need for the development of high‐calorie foods, including culinary oils. The seeds of oil crops contain high‐energy density oil composed of triacylglycerides (TAGs) at up to 80% by dry mass. However, maize (Zea mays L.) seeds are relatively poor in calorie and nutritional values. Therefore, in this report, we address this constraint via metabolic engineering to improve maize seed lipids including TAG and seed TAG nutritional values by overexpression of three major genes, including: (i) the Arabidopsis thaliana (L.) Heynh. diacylglycerol acyltransferase 1 (AtDGAT1), a gene that catalyzes the TAG biosynthesis final step prior to packaging of TAGs into oil bodies; (ii) the transcription factor WRINKLED 1 (WRI1), which promotes the regulation of the expression of genes involved in fatty acid biosynthesis; and (i) the A. thaliana oleosin (AtOleosin) gene, a gene coding for a protein that protects TAGs from degradation. The overexpression of the above three genes, and probably certain unintentional in vitro culture genetic variabilities, resulted in 117% increase of seed TAGs and 25% increase in total oil contents when compared with the wild‐type control corn seeds. In addition, the above genetic modifications led to major shifts in the fatty acid profiles in favor of human health.

Tryptophan (TRP) is a critical amino acid for biological function, with over 95% being metabolized through the enzymatic kynurenine pathway. Studies suggest roles for kynurenine metabolites in neurological disease states, ranging from depression, schizophrenia to Alzheimer’s and Parkinson’s diseases. We developed a method to detect and resolve TRP, kynurenine (KYN), serotonin (5-HT), kynurenic acid (KYNA), 3-hydroxykynurenine (3-HK), 3-hydroxyanthranilic acid (3-HAA), picolinic acid (PIC), quinolinic acid (QUIN), nicotinic acid (NIC), and nicotinamide (NTA). The method was developed to include kynurenine metabolites as well as resolve PIC from NIC, an isomer of PIC that is a source of nicotinamide adenine dinucleotide (NAD) production alongside QUIN and NTA.

Background: Interannual variability in precipitation, particularly drought, can affect lignocellulosic crop biomass yields and composition, and is expected to increase biofuel yield variability. However, the effect of precipitation on downstream fermentation processes has never been directly characterized. In order to investigate the impact of interannual climate variability on biofuel production, corn stover and switchgrass were collected during 3 years with significantly different precipitation profiles, representing a major drought year (2012) and 2 years with average precipitation for the entire season (2010 and 2013). All feedstocks were AFEX (ammonia fiber expansion)-pretreated, enzymatically hydrolyzed, and the hydrolysates separately fermented using xylose-utilizing strains of Saccharomyces cerevisiae and Zymomonas mobilis. A chemical genomics approach was also used to evaluate the growth of yeast mutants in the hydrolysates.Results: While most corn stover and switchgrass hydrolysates were readily fermented, growth of S. cerevisiae was completely inhibited in hydrolysate generated from drought-stressed switchgrass. Based on chemical genomics analysis, yeast strains deficient in genes related to protein trafficking within the cell were significantly more resistant to the drought-year switchgrass hydrolysate. Detailed biomass and hydrolysate characterization revealed that switchgrass accumulated greater concentrations of soluble sugars in response to the drought and these sugars were subsequently degraded to pyrazines and imidazoles during ammonia-based pretreatment. When added ex situ to normal switchgrass hydrolysate, imidazoles and pyrazines caused anaerobic growth inhibition of S. cerevisiae.Conclusions: In response to the osmotic pressures experienced during drought stress, plants accumulate soluble sugars that are susceptible to degradation during chemical pretreatments. For ammonia-based pretreatment, these sugars degrade to imidazoles and pyrazines. These compounds contribute to S. cerevisiae growth inhibition in drought-year switchgrass hydrolysate. This work discovered that variation in environmental conditions during the growth of bioenergy crops could have significant detrimental effects on fermentation organisms during biofuel production. These findings are relevant to regions where climate change is predicted to cause an increased incidence of drought and to marginal lands with poor water-holding capacity, where fluctuations in soil moisture may trigger frequent drought stress response in lignocellulosic feedstocks.

RATIONALE:Radical-directed dissociation techniques provide structural information which is complementary to that from conventional collision-induced dissociation (CID). The analysis of phosphopeptide anions is warranted due to their relatively acidic character. As femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) is uniquely initiated by field ionization, an investigation is warranted to determine whether fsLID may provide novel analytical utility for phosphopeptide anions.METHODS:Twenty-three synthetic deprotonated phosphopeptide anions were introduced into a three-dimensional quadrupole ion trap mass spectrometer via electrospray ionization. The ion trap was interfaced with a near-IR (802 nm) ultrashort-pulsed (35 fs FWHM) ultrahigh-powered (peak power ~10(14)  W/cm(2)) laser system. Performance comparisons are made with other techniques applied to phosphopeptide anion analysis, including CID, electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), activated electron photodetachment dissociation (activated-EPD), and ultraviolet photodissociation (UVPD).RESULTS:FsLID-MS/MS of multiply deprotonated phosphopeptide anions provides sequence information via phosphorylation-intact a/x ions in addition to other sequence ions, satellite ions, and side-chain losses. Novel fragmentation processes include selective c-ion formation N-terminal to Ser/Thr and a phosphorylation-specific correlation between xn -98 ion abundances and phosphorylation at the n(th) residue. Sequencing-quality data required about 30 s of signal averaging. fsLID-MS/MS of singly deprotonated phosphopeptides did not yield product anions with stable trajectories, despite significant depletion of the precursor.CONCLUSIONS:Multiply deprotonated phosphopeptide anions were sequenced via negative-mode fsLID-MS/MS, with phosphosite localization facilitated by a/x ion series in addition to diagnostic x(n)-98 ions. fsLID-MS/MS is qualitatively competitive with other techniques. Further efficiency enhancements (e.g., implementation on a linear trap or/and higher pulse frequencies) may permit sequence analyses on chromatographic timescales.

Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.

To develop an improved understanding of the regulatory role that post-translational modifications (PTMs) involving phosphorylation play in the maintenance of normal cellular function, tandem mass spectrometry (MS/MS) strategies coupled with ion activation techniques such as collision-induced dissociation (CID) and electron-transfer dissociation (ETD) are typically employed to identify the presence and site-specific locations of the phosphate moieties within a given phosphoprotein of interest. However, the ability of these techniques to obtain sufficient structural information for unambiguous phosphopeptide identification and characterization is highly dependent on the ion activation method employed and the properties of the precursor ion that is subjected to dissociation. Herein, we describe the application of a recently developed alternative ion activation technique for phosphopeptide analysis, termed femtosecond laser-induced ionization/dissociation (fs-LID). In contrast to CID and ETD, fs-LID is shown to be particularly suited to the analysis of singly protonated phosphopeptide ions, yielding a wide range of product ions including a, b, c, x, y, and z sequence ions, as well as ions that are potentially diagnostic of the positions of phosphorylation (e.g., ‘a n+1–98’). Importantly, the lack of phosphate moiety losses or phosphate group ‘scrambling’ provides unambiguous information for sequence identification and phosphorylation site characterization. Therefore, fs-LID-MS/MS can serve as a complementary technique to established methodologies for phosphoproteomic analysis.

In recent years, it has become increasingly interesting to understand the performance of mass spectrometers at pressures much higher than those employed with conventional operating conditions. This interest has been driven by several influences, including demand for the development of reduced-power miniature mass spectrometers, desire for improved ion transfer into and through mass spectrometers, enhanced-yield preparative mass separations, and mass filtering at the atmospheric pressure interface. In this study, an instrument was configured to allow for the performance characterization of a rectilinear ion trap (RIT) at pressures up to 50 mtorr with air used as the buffer gas. The mass analysis efficiency, mass resolution, isolation efficiency, and collision-induced dissociation (CID) efficiency were evaluated at pressures ranging from 1 to 50 mtorr. The extent of degradation of mass resolution, isolation efficiency and ion stability as functions of pressure were characterized. Also, the optimal resonance ejection conditions were obtained at various pressures. Operations at 50 mtorr demonstrated improved CID efficiency in addition to peak widths of 2 and 5 m/z units (full width at half-maximum, FWHM) for protonated caffeine (m/z 195) and Ultramark (m/z 1521) respectively.

The design and operation of an annular array of parallel, miniature rectilinear ion traps (RITs) is discussed. Stereolithography apparatus (SLA), a previously validated method for ion trap fabrication, was applied here to construct an array of mass analyzers and their mounting hardware. Two versions of the array were tested, using either six or twelve stretched RITs (x(0) = 1.66 mm, y(0) = 1.33 mm, z = 16.66 mm) mounted in parallel about the circumference of a circle with the interior and exterior x-electrode planes oriented tangential to the inner and outer annulus rings, respectively. The arrangement of the ion traps is such that the ions are radially ejected just above the throat of a centrally located electron multiplier detector into which they are accelerated. The mass analyzer array was mounted in a custom vacuum manifold. The resolution, mass-to-charge ratio (m/z) range, and MS/MS capabilities were tested using electrospray ionization (ESI). The devices were tested in two configurations: (i) separate ion sources for each trap, and (ii) a single ion source for the entire array.

A waveform isolation method is described for the mass-selective transmission of ions through quadrupole mass filters, and it is implemented on a new tandem mass analyzer instrument. The method features the application of broad-band waveforms comprising appropriate frequencies to cause mass-selective instability in ions of particular mass-to-charge (m/z) and to transmit all others. The experiment is implemented in a tandem quadrupole system in which the first mass filter is a rectilinear ion trap (RIT) operated in a continuous mass-selective mode to transmit ions of ions of one or more arbitrarily selected m/z value(s). The second analyzer was used to verify the quality of the mass selection achieved using the first analyzer via conventional quadrupole ion trap mass-selective instability scanning. A new subtype of product ion tandem mass spectrometry (MS/MS) scan, termed the summed product ion scan, is demonstrated with a mixture of biological compounds. It is used to characterize product ions arising after simultaneous isolation and collisional activation of multiple precursor species, in this case ions of the same analyte generated in different charge states. The summed product ion scan can be useful for enhancing sensitivity for the analyte of interest or for providing more comprehensive information about an analyte than is available by monitoring a single ionized form of the analyte. The analytical performance of the waveform isolation method is tested using simple drug mixtures, and its potential for increasing overall yields in preparative mass spectrometry is explored briefly. It is shown that efficiencies of ca. 70% of ion transfer to a surface for ion soft landing surface can be achieved. The upper mass range is limited by axial acceleration arising from the stretched geometry, and one solution to this problem is provided.

The mass-selective manipulation of ions at elevated pressure, including mass analysis, ion isolation, or excitation, is of great interest for the development of mass spectrometry instrumentation, particularly for systems in which ion traps are employed as mass analyzers or storage devices. While experimental exploration of high-pressure mass analysis is limited by various difficulties, such as ion detection or electrical discharge at high-pressure, theoretical methods have been developed in this work to study ion/neutral collision effects within quadrupole ion traps and to explore their performance at pressures up to 1 Torr. Ion trapping, isolation, excitation, and resonance ejection were investigated over a wide pressure range. The theoretically calculated data were compared with available experimental data for pressures up to 50 mTorr, allowing the prediction of ion trap performance at pressures more than 10 times higher.

Time resolved measurements show that during a desorption electrospray ionization (DESI) experiment, the current initially rises sharply, followed by an exponential decrease to a relatively steady current. When the high voltage on the spray emitter is switched off, the current drops to negative values, suggesting that the direction of current flow in the equivalent DESI circuit is reversed. These data demonstrate that the DESI source behaves as a dc capacitor and that the addition of a surface between the sprayer and the counter electrode in DESI introduces a new electrically active element into the system. The charging and discharging behavior was observed using different surfaces and it could be seen both by making current measurements on a plate at the entrance to the mass spectrometer as well as by measuring ion current in the linear ion trap within the vacuum system of the mass spectrometer. The magnitude of the steady state current obtained without analyte present on the surface is different for different surface materials, and different capacitor time constants of the equivalent RC circuits were calculated for different DESI surfaces. The PTFE surface has by far the greatest time constant and is also able to produce the highest DESI currents. Surface properties play a crucial role in charge transfer during DESI in addition to the effects of the chemical properties of the analyte. It is suggested that surface energy (wettability) is an important factor controlling droplet behavior on the surface. The experimental data are correlated with critical surface tension values of different materials. It is proposed, based on the results presented, that super-hydrophobic materials with extremely high contact angles have the potential to be excellent DESI substrates. It is also demonstrated, using the example of the neurotransmitter dopamine, that the surface charge that develops during a DESI-MS experiment can cause electrochemical oxidation of the analyte.

A novel linear ion trap (LIT) mass spectrometer with dual matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) ionization sources has been built in the MALDI-LIT-ESI configuration. The design features two independent ion source/ion optical channels connected to opposite ends of a single mass analyzer. The instrument consists of a commercial MALDI-LIT instrument modified by the addition of a home-built vacuum manifold, ion optical system, control electronics, and programming necessary to couple an atmospheric pressure interface to the commercial instrument. In addition to the added ESI functionality, the capabilities of the system also include simultaneous dual-channel ion introduction and analysis and high-duty cycle electronic switching (<1 s) between ion channels. Analytical and ion chemical applications of the dual-source system are explored. One analytical application is the enhanced protein sequence coverage achieved when using both ESI and MALDI to examine a tryptic digest of a six-protein mixture. The differences in the efficiency with which peptides in a mixture are ionized by the two methods give improved sequence coverage when both are applied. Other analytical applications include the use of the ions from one source as intensity or mass standards for the analyte ions from the other. An ion chemistry application involves the use of energy-resolved tandem mass spectrometry (MS/MS) to seek evidence for the generation of isomeric ions from a particular compound using the two ionization methods. A high level of agreement was achieved between the MS/MS spectra recorded under a variety of conditions after ESI and MALDI ionization; this provides evidence of the reproducibility and internal consistency of data from the dual source instrument. However, each of the peptides examined generated identical populations of structures in the two ionization methods under our conditions which are interpreted as involving slow cooling into the most stable minimum on the potential energy surface.

Companies today are continuously improving their efforts to incorporate an environmental management system (EMS) in their everyday operations and work practices, with an emphasis on identifying and reducing risks. Risks may include the cost of enforcement penalties, potential workplace dangers to employees, or cleanup liabilities due to past or present practices. Environmental auditing is an effective tool commonly used to enhance an EMS. Typically, there are two levels of auditing: (1) a review of management systems and (2) a review of compliance with regulatory requirements. There is yet another intermediate level of auditing that is more focused than management systems or compliance audits—compliance delivery systems (CDS) audits. This article examines the elements making up these systems for improving compliance performance and provides a „ready to use”︁ checklist of items for managers to begin implementation.