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Background: Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are prominent candidate biocatalysts that, together, can enable the direct biotic conversion of lignocellulosic biomass to ethanol. The imbalance and suboptimal turnover rates of redox cofactors are currently hindering engineering efforts to achieve higher bioproductivity in both organisms. Measuring relevant intracellular cofactor concentrations will help understand redox state of these cofactors and help identify a strategy to overcome these limitations; however, metabolomic determinations of these labile metabolites have historically proved challenging., Results: Through our validations, we verified the handling and storage stability of these metabolites, and verified extraction matrices and extraction solvent were not suppressing mass spectrometry signals. We recovered adenylate energy charge ratios (a main quality indicator) above 0.82 for all extractions. NADH/NAD+ values of 0.26 and 0.04 for an adhE -deficient strain of C. thermocellum and its parent, respectively, reflect the expected shift to a more reduced redox potential when a species lacks the ability to re-oxidize NADH by synthesizing ethanol. This method failed to yield reliable results with C. bescii and poor-growing strains of T. saccharolyticum., Conclusions: Our validated protocols demonstrate and validate the extraction and analysis of selected redox and energy-related metabolites from two candidate consolidated bioprocessing biocatalysts, C. thermocellum and T. saccharolyticum . This development and validation highlights the important, but often neglected, need to optimize and validate metabolomic protocols when adapting them to new cell or tissue types.

Cell-free protein synthesis (CFPS) has the potential to produce enzymes, therapeutic agents, and other proteins, while circumventing difficulties associated with in vivo heterologous expression. However, the contents of the cell-free extracts used to carry out synthesis are generally not characterized, which hampers progress toward enhancing yield or functional activity of the target protein. We explored the utility of mass spectrometry (MS)-based proteomics for characterizing the bacterial extracts used for transcribing and translating gene sequences into proteins as well as the products of CFPS reactions. Full proteome experiments identified over 1000 proteins per reaction. The complete set of proteins necessary for transcription and translation were found, demonstrating the ability to define potential metabolic capabilities of the extract. Further, MS-based techniques allowed characterization of the CFPS product and provided insight into the synthesis reaction and potential functional activity of the product. These capabilities were demonstrated using two different CFPS products, the commonly used standard green fluorescent protein (GFP, 27 kDa) and the polyketide synthase DEBS1 (394 kDa). For the large, multidomain DEBS1, substantial premature termination of protein translation was observed. Additionally, MS/MS analysis, as part of a conventional full proteomics workflow, identified post-translational modifications, including the chromophore in GFP, as well as the three phosphopantetheinylation sites in DEBS1. A hypothesis-driven approach focused on these three sites identified that all were correctly modified for DEBS1 expressed in vivo but with less complete coverage for protein expressed in CFPS reactions. These post-translational modifications are essential for functional activity, and the ability to identify them with mass spectrometry is valuable for judging the success of the CFPS reaction. Collectively, the use of MS-based proteomics will prove advantageous for advancing the application of CFPS and related techniques.

Elucidation of protein-protein interactions can provide new knowledge on protein function. Enrichments of affinity-tagged (or "bait") proteins with interaction partners generally include background, nonspecific protein artifacts. Furthermore, in vivo bait expression may introduce additional artifacts arising from altered physiology or metabolism. In this study, we compared these effects for chromosome and plasmid encoding strategies for bait proteins in two microbes: Escherichia coli and Rhodopseudomonas palustris. Differential metabolic labeling of strains expressing bait protein relative to the wild-type strain in each species allowed comparison by liquid chromatography tandem mass spectrometry (LC-MS-MS). At the local level of the protein complex, authentic interacting proteins of RNA polymerase (RNAP) were successfully discerned from artifactual proteins by the isotopic differentiation of interactions as random or targeted (I-DIRT, Tackett, A. J.; et al. J. Proteome Res. 2005, 4, 1752-1756). To investigate global effects of bait protein production, we compared proteomes from strains harboring a plasmid encoding an affinity-tagged subunit (RpoA) of RNAP with the corresponding wild-type strains. The RpoA abundance ratios of 0.8 for R. palustris and 1.7 for E. coli in plasmid strains versus wild-type indicated only slightly altered expression. While most other proteins also showed no appreciable difference in abundance, several that did show altered levels were involved in amino acid metabolism. Measurements at both local and global levels proved useful for evaluating in vitro and in vivo artifacts of plasmid-encoding strategies for bait protein expression.

The Scent Transfer Unit (STU-100) is a portable vacuum that uses airflow through a sterile gauze pad to capture a volatiles profile over evidentiary items for subsequent canine presentation to assist law enforcement personnel. This device was evaluated to determine its ability to trap and release organic compounds at ambient temperature under controlled laboratory conditions. Gas chromatography-mass spectrometry (GC-MS) analyses using a five-component volatiles mixture in methanol injected directly into a capture pad indicated that compound release could be detected initially and 3 days after the time of collection. Additionally, 15 compounds of a 39-component toxic organic gaseous mixture (10-1000 parts per billion by volume [p.p.b.(v)]) were trapped, released, and detected in the headspace of a volatiles capture pad after being exposed to this mixture using the STU-100 with analysis via GC-MS. Component release efficiencies at ambient temperature varied with the analyte; however, typical values of c. 10% were obtained. Desorption at elevated temperatures of reported human odor/scent chemicals and colognes trapped by the STU-100 pads was measured and indicated that the STU-100 has a significant trapping efficiency at ambient temperature. Multivariate statistical analysis of subsequent mass spectral patterns was also performed.

A self-aspirating heated nebulizer probe is described and demonstrated for use in the direct analysis of analytes on surfaces and in liquid samples by atmospheric pressure chemical ionization (APCI) mass spectrometry. Functionality and performance of the probe as a self-aspirating APCI source is demonstrated using reserpine and progesterone as test compounds. The utility of the probe to sample analytes directly from surfaces was demonstrated first by scanning development lanes of a reversed-phase thin-layer chromatography plate in which a three-component dye mixture, viz., Fat Red 7B, Solvent Green 3, and Solvent Blue 35, was spotted and the components were separated. Development lanes were scanned by the sampling probe operated under computer control (x, y plane) while full-scan mass spectra were recorded using a quadrupole ion trap mass spectrometer. In addition, the ability to sample the surface of pharmaceutical tablets (viz., Extra Strength Tylenol and Evista tablets) and to detect the active ingredients (acetaminophen and raloxifene, respectively) selectively was demonstrated using tandem mass spectrometry (MS/MS). Finally, the capability to sample analyte solutions from the wells of a 384-well microtiter plate and to perform quantitative analyses using MS/MS detection was illustrated with cotinine standards spiked with cotinine-d3 as an internal standard., (Published in 2005 by John Wiley & Sons, Ltd.)

The inherent electrochemistry occurring at the emitter electrode of an electrospray ion source was effectively controlled by incorporating a three-electrode controlled-potential electrochemical cell into the controlled-current electrospray emitter circuit. Two different basic cell designs were investigated to accomplish this control, namely, a planar flow-by working electrode and a porous flow-through working electrode design, each operated with a potentiostat floated at the electrospray high voltage. Control of the analyte electrochemistry was tested using the indole alkaloid reserpine, which is often used to test the specifications of electrospray mass spectrometry instrumentation. Reserpine was relatively easy to oxidize (E(p) = 0.73 V vs Ag/AgCl) in the acidic electrospray medium (acetonitrile/water 1:1 v/v, 5.0 mM ammonium acetate, 0.75 vol % acetic acid) and was oxidized when the conventional electrospray emitter was used at low solution flow rate. With the proper cell auxiliary electrode configuration and adjustment of the working electrode potential, it was found that reserpine oxidation could be "turned off" at flow rates as low as 2.5 microL/min as well as at flow rates as high as 30-40 microL/min. Just as important, it was also possible to "turn on" essentially 100% oxidation of reserpine in this flow rate range. The area of the auxiliary electrode along with flow rate, which affect mass transport of analytes to this electrode, were found to be critical in controlling the electrochemical reactions in the emitter cell. Such control over analyte electrochemical reactions in the emitter has been difficult or impossible to achieve with a conventional electrospray emitter. This control is paramount in obtaining experimental results free from electrochemically generated artifacts of the analyte or in exploiting electrochemical reactions involving the analyte to analytical advantage.

A thin-channel, planar electrode emitter device is described and utilized for the study and control of electrochemical oxidation of analytes at the emitter electrode in an electrospray ion source. For analytes that are not particularly susceptible to oxidation, the planar electrode device functions analytically in a manner similar to emitter systems that utilize the more common stainless steel tubular electrodes. For more easily oxidized analytes, the device provides the means to achieve near 100% oxidation efficiency or to completely eliminate analyte oxidation through simple and rapid changes in electrode material, electrode area, electrode covering, channel height above the electrode, or solution flow rate. Compared to the use of tubular electrodes, the planar electrode emitter system provides improved flexibility in altering the nature of the electrode area and material, as well as altering analyte mass transport to the electrode surface. Each of these parameters is critical in the control of electrochemical reactions and can be easily studied or exploited with this emitter electrode configuration.

This work investigates the chemical nature of fingerprints to ascertain whether differences in chemical composition or the existence of chemical markers can be used to determine personal traits, such as age, gender, and personal habits. This type of information could be useful for reducing the pool of potential suspects in criminal investigations when latent fingerprints are unsuitable for comparison by traditional methods. Fingertip residue that has been deposited onto a bead was extracted with a solvent such as chloroform. Samples were analyzed by gas chromatography/mass spectrometry (GC/MS). The chemical components identified include fatty acids, long chain fatty acid esters, cholesterol and squalene. The area ratios of ten selected components relative to squalene were calculated for a small preliminary experiment that showed a slight gender difference for three of these components. However, when the experiment was repeated with a larger, statistically designed experiment no significant differences between genders were detected for any of the component ratios. The multivariate Hotelling's T2 test that tested all ten-component ratios simultaneously also showed no gender differences at the 5% significance level.

Here we present a comprehensive method for proteome analysis that integrates both intact protein measurement ("top-down") and proteolytic fragment characterization ("bottom-up") mass spectrometric approaches, capitalizing on the unique capabilities of each method. This integrated approach was applied in a preliminary proteomic analysis of Shewanella oneidensis, a metal-reducing microbe of potential importance to the field of bioremediation. Cellular lysates were examined directly by the "bottom-up" approach as well as fractionated via anion-exchange liquid chromatography for integrated studies. A portion of each fraction was proteolytically digested, with the resulting peptides characterized by on-line liquid chromatography/tandem mass spectrometry. The remaining portion of each fraction containing the intact proteins was examined by high-resolution Fourier transform mass spectrometry. This "top-down" technique provided direct measurement of the molecular masses for the intact proteins and thereby enabled confirmation of post-translational modifications, signal peptides, and gene start sites of proteins detected in the "bottom-up" experiments. A total of 868 proteins from virtually every functional class, including hypotheticals, were identified from this organism.

Experiments are described that illustrate solvent oxidation, emitter electrode corrosion, and analyte oxidation in positive ion mode nano-electrospray mass spectrometry using a wire-in-a-capillary, bulk-loaded nano-electrospray emitter geometry. Time-lapsed color photography of pH and metal specific indicator solutions within operating nano-electrospray emitters, as well as temporal changes in the ions observed in the nano-electrospray mass spectra, are used to probe these reactions, judge their magnitude, and study the time dependent changes in solution composition and gas-phase ion signal brought about as a result of these electrochemical reactions. The significance of these observations for analytical applications of nano-electrospray mass spectrometry are discussed.

Protein ions of different mass and charge but similar mass-to-charge ratios are shown to undergo significantly different rates of differential neutralization, defined as the rate of change of charge with time, upon initiation of reactions with oppositely charged ions in the quadrupole ion trap. Overlapping charge state distributions arising from mixtures of ions of dissimilar charge are separated on the mass-to-charge scale at short reactions times. It is also demonstrated that the time frame for near total neutralization, defined as charge reduction to the 1+ ion, is relatively insensitive to initial charge state. It is shown, for example, that the (M + 11H)(11+)-(M + 22H)22+ ions derived from horse skeletal muscle apomyoglobin yield the (M + H)+ ion as the major ion/ion reaction product over the same reaction period that largely converts doubly protonated bradykinin to the singly protonated species. Less than 25% of the bradykinin ions are expected to be totally neutralized when roughly 7% of the myoglobin ions are expected to be totally neutralized. The phenomenon of significantly different initial differential neutralization rates for ions of dissimilar charge, and the relative insensitivity to ion charge for total neutralization, can be used to advantage in strategies for protein ion mixture analysis.

The first observation of organic dications formed by multiple electron loss in electrospray mass spectra is reported. The dications of β-carotene, canthaxanthine, cobalt(II) octaethylporphyrin, and nicke(II) octaethylporphyrin were created in solution via chemical electrontransfer reactions and detected in the gas phase by electrospray ionization mass spectrometry (ES-MS) using a flow-injection experiment. The analytes were injected into a flowing solvent-oxidant stream (10 μL/min) composed of dried methylene chloride containing ≈ 0.1% by volume trifluoroacetic acid and 0.1% by volume antimony pentafluoride (SbF5). The dications created in this oxidizing solvent system were preserved for detection by rapidly transferring them from the reactive solvent-oxidant system to the gas phase, where, in the absence of the solvent system, they were "long-lived" and amenable to mass analysis. This work demonstrates means to produce ions novel to ES-MS and means to detect and study by ES-MS species that are short-lived in solution. In addition, this work shows that electrospray ionization can potentially be used to generate gas-phase dications for mass spectrometric study that are difficult to produce directly from gas-phase neutrals by other ionization techniques (e.g., M(2+) from β-carotene).

The ability to obtain daughter ion formulas via comparison of MS(n) spectra of parent ions containing only (12)C with those of parent ions with one (13)C (from the natural (13)C abundance) is shown for cases in which isobaric interferences with the (13)C-containing ion preclude the use of the conventional tandem mass spectrometric approach. This method allows the presence of isobaric daughter ions to be ascertained, and unexpected, complex dissociation pathways to be identified. A three-dimensional quadrupole ion trap is used for these experiments. Its high tandem mass spectrometry efficiency makes possible this type of experiment.