High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Liquid ultraviolet matrix-assisted laser desorption/ionization - mass spectrometry for automated proteomic analysis

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet -- matrix-assisted laser desorption/ionisation -- mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. The low-femtomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydroxybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and low-mass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

Direct detection of dimethylstannylene and tetramethyldistannene in solution and the gas phase by laser flash photolysis of 1,1-dimethylstannacyclopent-3-enes

The photochemistry of 1,1-dimethyl- and 1,1,3,4-tetramethylstannacyclopent-3-ene (4a and 4b,respectively) has been studied in the gas phase and in hexane solution by steady-state and 193-nm laser flash photolysis methods. Photolysis of the two compounds results in the formation of 1,3-butadiene (from 4a) and 2,3-dimethyl-1,3-butadiene (from 4b) as the major products, suggesting that cycloreversion to yield dimethylstannylene (SnMe2) is the main photodecomposition pathway of these molecules. Indeed, the stannylene has been trapped as the Sn-H insertion product upon photolysis of 4a in hexane containing trimethylstannane. Flash photolysis of 4a in the gas phase affords a transient absorbing in the 450-520nm range that is assigned to SnMe2 by comparison of its spectrum and reactivity to those previously reported from other precursors. Flash photolysis of 4b in hexane solution affords results consistent with the initial formation of SnMe2 (lambda(max) approximate to 500 nm), which decays over similar to 10 mu s to form tetramethyldistannene (5b; lambda(max) approximate to 470 nm). The distannene decays over the next ca. 50 mu s to form at least two other longer-lived species, which are assigned to higher SnMe2 oligomers. Time-dependent DFT calculations support the spectral assignments for SnMe2 and Sn2Me4, and calculations examining the variation in bond dissociation energy with substituent (H, Me, and Ph) in disilenes, digermenes, and distannenes rule out the possibility that dimerization of SnMe2 proceeds reversibly. Addition of methanol leads to reversible reaction with SnMe2 to form a transient absorbing at lambda(max) approximate to 360 nm, which is assigned to the Lewis acid-base complex between SnMe2 and the alcohol.

What have we learnt about heavy carbenes through laser flash photolysis studies?

Time resolved gas-phase kinetic studies have contributed a great deal of fundamental information about the reactions and reactivity of heavy carbenes (silylenes, germylenes and stannylenes) during the past two decades. In this article we trace the development of our understanding through the mechanistic themes of intermediate complexes, third body assisted associations, catalysed reactions, non-observed reactions and substituent effects. Ab initio (quantum chemical) calculations have substantially assisted mechanistic interpretation and are discussed where appropriate. Trends in reactivity are identified and some signposts to future studies are indicated. This review, although detailed, is not comprehensive.

Liquid ultraviolet matrix-assisted laser desorption/ionization mass spectrometry for automated proteomic analysis

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet - matrix-assisted laser desorption/ ionisation - mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. U. Am. Soc. Mass Spectrom. 1998, 9, 166-174). The low-ferntomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydrox-ybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and lowmass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

High-throughput proteomics using matrix-assisted laser desorption/ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Thermoselective phase property of silica tethered with fluorinated chains for controlled 'release' and 'capture' of catalytic fluorous tin species

The temperature dependent mixing of organic and fluorous phases is one of the key principals of fluorous biphasic systems (FBS). Given the high cost of the perfluorous solvents and their impacts to the environment, it is apparent that elimination of these solvents in bulk quantity in the FBS is advantageous. We report for the first time, the surface coverage of silica with a fluorous solvent like material that traps (at ambient temperatures) and releases (at elevated temperatures) a fluorous tin bromide in organic solvent. Here, we demonstrate the catalytic utilisation of this species for the hydrocyclisation of 6-bromo-1-hexene with NaBH4. (C) 2002 Elsevier Science B.V. All rights reserved.

Oxidation of biogenic and water-soluble compounds in aqueous and organic aerosol droplets by ozone: a kinetic and product analysis approach using laser Raman tweezers

The results of an experimental study into the oxidative degradation of proxies for atmospheric aerosol are presented. We demonstrate that the laser Raman tweezers method can be used successfully to obtain uptake coeffcients for gaseous oxidants on individual aqueous and organic droplets, whilst the size and composition of the droplets is simultaneously followed. A laser tweezers system was used to trap individual droplets containing an unsaturated organic compound in either an aqueous or organic ( alkane) solvent. The droplet was exposed to gas- phase ozone and the reaction kinetics and products followed using Raman spectroscopy. The reactions of three different organic compounds with ozone were studied: fumarate anions, benzoate anions and alpha pinene. The fumarate and benzoate anions in aqueous solution were used to represent components of humic- like substances, HULIS; a alpha- pinene in an alkane solvent was studied as a proxy for biogenic aerosol. The kinetic analysis shows that for these systems the diffusive transport and mass accommodation of ozone is relatively fast, and that liquid- phase di. ffusion and reaction are the rate determining steps. Uptake coe. ffcients, g, were found to be ( 1.1 +/- 0.7) x 10(-5), ( 1.5 +/- 0.7) x 10 (-5) and ( 3.0 - 7.5) x 10 (-3) for the reactions of ozone with the fumarate, benzoate and a- pinene containing droplets, respectively. Liquid- phase bimolecular rate coe. cients for reactions of dissolved ozone molecules with fumarate, benzoate and a- pinene were also obtained: k(fumarate) = ( 2.7 +/- 2) x 10 (5), k(benzoate) = ( 3.5 +/- 3) x 10 (5) and k(alpha-pinene) = ( 1-3) x 10(7) dm(3) mol (-1) s (- 1). The droplet size was found to remain stable over the course of the oxidation process for the HULIS- proxies and for the oxidation of a- pinene in pentadecane. The study of the alpha- pinene/ ozone system is the first using organic seed particles to show that the hygroscopicity of the particle does not increase dramatically over the course of the oxidation. No products were detected by Raman spectroscopy for the reaction of benzoate ions with ozone. One product peak, consistent with aqueous carbonate anions, was observed when following the oxidation of fumarate ions by ozone. Product peaks observed in the reaction of ozone with alpha- pinene suggest the formation of new species containing carbonyl groups.

An integrated assessment of carbon dioxide capture and storage in the UK

Geological carbon dioxide storage (CCS) has the potential to make a significant contribution to the decarbonisation of the UK. Amid concerns over maintaining security, and hence diversity, of supply, CCS could allow the continued use of coal, oil and gas whilst avoiding the CO2 emissions currently associated with fossil fuel use. This project has explored some of the geological, environmental, technical, economic and social implications of this technology. The UK is well placed to exploit CCS with a large offshore storage capacity, both in disused oil and gas fields and saline aquifers. This capacity should be sufficient to store CO2 from the power sector (at current levels) for a least one century, using well understood and therefore likely to be lower-risk, depleted hydrocarbon fields and contained parts of aquifers. It is very difficult to produce reliable estimates of the (potentially much larger) storage capacity of the less well understood geological reservoirs such as non-confined parts of aquifers. With the majority of its large coal fired power stations due to be retired during the next 15 to 20 years, the UK is at a natural decision point with respect to the future of power generation from coal; the existence of both national reserves and the infrastructure for receiving imported coal makes clean coal technology a realistic option. The notion of CCS as a ‘bridging’ or ‘stop-gap’ technology (i.e. whilst we develop ‘genuinely’ sustainable renewable energy technologies) needs to be examined somewhat critically, especially given the scale of global coal reserves. If CCS plant is built, then it is likely that technological innovation will bring down the costs of CO2 capture, such that it could become increasingly attractive. As with any capitalintensive option, there is a danger of becoming ‘locked-in’ to a CCS system. The costs of CCS in our model for UK power stations in the East Midlands and Yorkshire to reservoirs in the North Sea are between £25 and £60 per tonne of CO2 captured, transported and stored. This is between about 2 and 4 times the current traded price of a tonne of CO2 in the EU Emissions Trading Scheme. In addition to the technical and economic requirements of the CCS technology, it should also be socially and environmentally acceptable. Our research has shown that, given an acceptance of the severity and urgency of addressing climate change, CCS is viewed favourably by members of the public, provided it is adopted within a portfolio of other measures. The most commonly voiced concern from the public is that of leakage and this remains perhaps the greatest uncertainty with CCS. It is not possible to make general statements concerning storage security; assessments must be site specific. The impacts of any potential leakage are also somewhat uncertain but should be balanced against the deleterious effects of increased acidification in the oceans due to uptake of elevated atmospheric CO2 that have already been observed. Provided adequate long term monitoring can be ensured, any leakage of CO2 from a storage site is likely to have minimal localised impacts as long as leaks are rapidly repaired. A regulatory framework for CCS will need to include risk assessment of potential environmental and health and safety impacts, accounting and monitoring and liability for the long term. In summary, although there remain uncertainties to be resolved through research and demonstration projects, our assessment demonstrates that CCS holds great potential for significant cuts in CO2 emissions as we develop long term alternatives to fossil fuel use. CCS can contribute to reducing emissions of CO2 into the atmosphere in the near term (i.e. peak-shaving the future atmospheric concentration of CO2), with the potential to continue to deliver significant CO2 reductions over the long term.

Equivalent noise level generated by drilling onto the ossicular chain as measured by laser Doppler vibrometry: A temporal bone study

Background: Inadvertent drilling on the ossicular chain is one of the causes of sensorineural hearing loss (HL) that may follow tympanomastoid surgery. A high-frequency HL is most frequently observed. It is speculated that the HL is a result of vibration of the ossicular chain resembling acoustic noise trauma. It is generally considered that using a large cutting burr is more likely to cause damage than a small diamond burr. Aim: The aim was to investigate the equivalent noise level and its frequency characteristics generated by drilling onto the short process of the incus in fresh human temporal bones. Methods and Materials: Five fresh cadaveric temporal bones were used. Stapes displacement was measured using laser Doppler vibrometry during short drilling episodes. Diamond. and cutting burrs of different diameters were used. The effect of the drilling on stapes footplate displacement was compared with that generated by an acoustic signal. The equivalent noise level (dB sound pressure level equivalent [SPL eq]) was thus calculated. Results: The equivalent noise levels generated ranged from 93 to 125 dB SPL eq. For a 1-mm cutting burr, the highest equivalent noise level was 108 dB SPL eq, whereas a 2.3-mm cutting burr produced a maximal level of 125 dB SPL eq. Diamond burrs generated less noise than their cutting counterparts, with a 2.3-mm diamond burr producing a highest equivalent noise level of 102, dB SPL eq. The energy of the noise increased at the higher end of the frequency spectrum, with a 2.3-mm cutting burr producing a noise level of 105 dB SPL eq at 1 kHz and 125 dB SPL eq at 8 kHz. In contrast, the same sized diamond burr produced 96 dB SPL eq at 1 kHz and 99 dB at 8 kHz. Conclusion:This study suggests that drilling on the ossicular chain can produce vibratory force that is analogous with noise levels known to produce acoustic trauma. For the same type of burr, the larger the diameter, the greater the vibratory force, and for the same size of burr, the cutting burr creates more vibratory force than the diamond burr. The cutting burr produces greater high-frequency than lower-frequency vibratory energy.

Techno-economic modelling and cost functions of CO2 capture processes

The paper presents the techno-economic modelling of CO2 capture process in coal-fired power plants. An overall model is being developed to compare carbon capture and sequestration options at locations within the UK, and for studies of the sensitivity of the cost of disposal to changes in the major parameters of the most promising solutions identified. Technological options of CO2 capture have been studied and cost estimation relationships (CERs) for the chosen options calculated. Created models are related to the capital, operation and maintenance cost. A total annualised cost of plant electricity output and amount of CO2 avoided have been developed. The influence of interest rates and plant life has been analysed as well. The CERs are included as an integral part of the overall model.

Life cycle GHG assessment of fossil fuel power plants with carbon capture and storage

The evaluation of life cycle greenhouse gas emissions from power generation with carbon capture and storage (CCS) is a critical factor in energy and policy analysis. The current paper examines life cycle emissions from three types of fossil-fuel-based power plants, namely supercritical pulverized coal (super-PC), natural gas combined cycle (NGCC) and integrated gasification combined cycle (IGCC), with and without CCS. Results show that, for a 90% CO2 capture efficiency, life cycle GHG emissions are reduced by 75-84% depending on what technology is used. With GHG emissions less than 170 g/kWh, IGCC technology is found to be favorable to NGCC with CCS. Sensitivity analysis reveals that, for coal power plants, varying the CO2 capture efficiency and the coal transport distance has a more pronounced effect on life cycle GHG emissions than changing the length of CO2 transport pipeline. Finally, it is concluded from the current study that while the global warming potential is reduced when MEA-based CO2 capture is employed, the increase in other air pollutants such as NOx and NH3 leads to higher eutrophication and acidification potentials.