Protein oxidation:role in signalling and detection by mass spectrometry

Proteins can undergo a wide variety of oxidative post-translational modifications (oxPTM); while reversible modifications are thought to be relevant in physiological processes, non-reversible oxPTM may contribute to pathological situations and disease. The oxidant is also important in determining the type of oxPTM, such as oxidation, chlorination or nitration. The best characterized oxPTMs involved in signalling modulation are partial oxidations of cysteine to disulfide, glutathionylated or sulfenic acid forms that can be reversed by thiol reductants. Proline hydroxylation in HIF signalling is also quite well characterized, and there is increasing evidence that specific oxidations of methionine and tyrosine may have some biological roles. For some proteins regulated by cysteine oxidation, the residues and molecular mechanism involved have been extensively studied and are well understood, such as the protein tyrosine phosphatase PTP1B and MAP3 kinase ASK1, as well as transcription factor complex Keap1-Nrf2. The advances in understanding of the role oxPTMs in signalling have been facilitated by advances in analytical technology, in particular tandem mass spectrometry techniques. Combinations of peptide sequencing by collisionally induced dissociation and precursor ion scanning or neutral loss to select for specific oxPTMs have proved very useful for identifying oxidatively modified proteins and mapping the sites of oxidation. The development of specific labelling and enrichment procedures for S-nitrosylation or disulfide formation has proved invaluable, and there is ongoing work to establish analogous methods for detection of nitrotyrosine and other modifications.

Investigation and development of techniques for the characterisation of the synthetic/biological interface

The purpose of this study is to increase our knowledge of the nature of the surface properties of polymeric materials and improve our understanding of how these factors influence the deposition of proteins to form a reactive biological/synthetic interface. A number of surface analytical techniques were identified as being of potential benefit to this investigation and included in a multidisciplinary research program. Cell adhesion in culture was the primary biological sensor of surface properties, and it showed that the cell response to different materials can be modified by adhesion promoting protein layers: cell adhesion is a protein-mediated event. A range of surface rugosity can be produced on polystyrene, and the results presented here show that surface rugosity does not play a major role in determining a material's cell adhesiveness. Contact angle measurements showed that surface energy (specifically the polar fraction) is important in promoting cell spreading on surfaces. The immunogold labelling technique indicated that there were small, but noticeable differences, between the distribution of proteins on a range of surfaces. This study has shown that surface analysis techniques have different sensitivities in terms of detection limits and depth probed, and these are important in determining the usefulness of the information obtained. The techniques provide information on differing aspects of the biological/synthetic interface, and the consequence of this is that a range of techniques is needed in any full study of such a complex field as the biomaterials area.

Water detection in jet fuel using a polymer optical fibre Bragg grating

Water is a common impurity of jet fuel, and can exist in three forms: dissolved in the fuel, as a suspension and as a distinct layer at the bottom of the fuel tank. Water cannot practically be eliminated from fuel but must be kept to a minimum as large quantities can cause engine problems, particularly when frozen, and the interface between water and fuel acts as a breeding ground for biological contaminants. The quantities of dissolved or suspended water are quite small, ranging from about 10 ppm to 150 ppm. This makes the measurement task difficult and there is currently a lack of a convenient, electrically passive system for water-in-fuel monitoring; instead the airlines rely on colorimetric spot tests or simply draining liquid from the bottom of fuel tanks. For all these reason, people have explored different ways to detect water in fuel, however all these approaches have problems, e.g. they may not be electrically passive or they may be sensitive to the refractive index of the fuel. In this paper, we present a simple, direct and sensitive approach involving the use of a polymer optical fibre Bragg grating to detect water in fuel. The principle is that poly(methyl methacrylate) (PMMA) can absorb moisture from its surroundings (up to 2% at 23 °C), leading to both a swelling of the material and an increase in refractive index with a consequent increase in the Bragg wavelength of a grating inscribed in the material.

Evaluation of remote sensing for the detection of landfill gas and leachate in an urban environment

The technique of remote sensing provides a unique view of the earth's surface and considerable areas can be surveyed in a short amount of time. The aim of this project was to evaluate whether remote sensing, particularly using the Airborne Thematic Mapper (ATM) with its wide spectral range, was capable of monitoring landfill sites within an urban environment with the aid of image processing and Geographical Information Systems (GIS) methods. The regions under study were in the West Midlands conurbation and consisted of a large area in what is locally known as the Black Country containing heavy industry intermingled with residential areas, and a large single active landfill in north Birmingham. When waste is collected in large volumes it decays and gives off pollutants. These pollutants, landfill gas and leachate (a liquid effluent), are known to be injurious to vegetation and can cause stress and death. Vegetation under stress can exhibit a physiological change, detectable by the remote sensing systems used. The chemical and biological reactions that create the pollutants are exothermic and the gas and leachate, if they leave the waste, can be warmer than their surroundings. Thermal imagery from the ATM (daylight and dawn) and thermal video were obtained and used to find thermal anomalies on the area under study. The results showed that vegetation stress is not a reliable indicator of landfill gas migration, as sites within an urban environment have a cover too complex for the effects to be identified. Gas emissions from two sites were successfully detected by all the thermal imagery with the thermal ATM being the best. Although the results were somewhat disappointing, recent technical advancements in the remote sensing systems used in this project would allow geo-registration of ATM imagery taken on different occasions and the elimination of the effects of solar insolation.

Redox signalling and detection of protein oxidation by mass spectrometry

It is now recognised that redox control of proteins plays an important role in many signalling pathways both in health and disease. Proteins can undergo a wide variety of oxidative post-translational modifications (oxPTM); while the reversible modifications are thought to be most important in physiological processes, non-reversible oxPTM may contribute to pathological situations and disease. The oxidant is also important in determining the type of oxPTM (chlorination, nitration, etc.), and the susceptibilities of residues vary depending on their structural location. The best characterized oxPTMs involved in signalling modulation are partial oxidations of cysteine to the disulfide, glutathionylated or sulfenic acid forms, but there is increasing evidence that specific oxidations of methionine and tyrosine may have some biological roles. Well understood examples of oxidative regulation include protein tyrosine phosphatases, e.g. PTP1B/C, and members of the MAPK pathways such as MEKK1 and ASK1. Transcription factors such as NFkB and Nrf-2 are also regulated by redox-active cysteines. Improved methods for analysing specific oxPTMs in biological samples are critical for understanding the physiological and pathological roles of these changes, and tandem or MS3 mass spectrometry techniques interfaced with nano-LC separation are being now used. MS3 fragmentation markers for a variety of oxidized residues including tyrosine, tryptophan and proline have been identified, and a precursor ion scanning method that allows the selective identification of these oxPTMs in complex samples has been developed. Such advances in technology offer potential for biomarker development, disease diagnosis and understanding pathology.

Optical fibre-based detection of DNA hybridization

A dual-peak LPFG (long-period fibre grating), inscribed in an optical fibre, has been employed to sense DNA hybridization in real time, over a 1 h period. One strand of the DNA was immobilized on the fibre, while the other was free in solution. After hybridization, the fibre was stripped and repeated detection of hybridization was achieved, so demonstrating reusability of the device. Neither strand of DNA was fluorescently or otherwise labelled. The present paper will provide an overview of our early-stage experimental data and methodology, examine the potential of fibre gratings for use as biosensors to monitor both nucleic acid and other biomolecular interactions and then give a summary of the theory and fabrication of fibre gratings from a biological standpoint. Finally, the potential of improving signal strength and possible future directions of fibre grating biosensors will be addressed.

Post-translational modifications and mass spectrometry detection

In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry. © 2013 Elsevier Inc.

Water detection in jet fuel using a polymer optical fibre Bragg grating

Water is a common impurity of jet fuel, and can exist in three forms: dissolved in the fuel, as a suspension and as a distinct layer at the bottom of the fuel tank. Water cannot practically be eliminated from fuel but must be kept to a minimum as large quantities can cause engine problems, particularly when frozen, and the interface between water and fuel acts as a breeding ground for biological contaminants. The quantities of dissolved or suspended water are quite small, ranging from about 10 ppm to 150 ppm. This makes the measurement task difficult and there is currently a lack of a convenient, electrically passive system for water-in-fuel monitoring; instead the airlines rely on colorimetric spot tests or simply draining liquid from the bottom of fuel tanks. For all these reason, people have explored different ways to detect water in fuel, however all these approaches have problems, e.g. they may not be electrically passive or they may be sensitive to the refractive index of the fuel. In this paper, we present a simple, direct and sensitive approach involving the use of a polymer optical fibre Bragg grating to detect water in fuel. The principle is that poly(methyl methacrylate) (PMMA) can absorb moisture from its surroundings (up to 2% at 23 °C), leading to both a swelling of the material and an increase in refractive index with a consequent increase in the Bragg wavelength of a grating inscribed in the material.

Detection of phospholipid oxidation in oxidatively stressed cells by reversed-phase HPLC coupled with positive-ionization electrospray MS

Measurement of lipid peroxidation is a commonly used method of detecting oxidative damage to biological tissues, but the most frequently used methods, including MS, measure breakdown products and are therefore indirect. We have coupled reversed-phase HPLC with positive-ionization electrospray MS (LC-MS) to provide a method for separating and detecting intact oxidized phospholipids in oxidatively stressed mammalian cells without extensive sample preparation. The elution profile of phospholipid hydroperoxides and chlorohydrins was first characterized using individual phospholipids or a defined phospholipid mixture as a model system. The facility of detection of the oxidized species in complex mixtures was greatly improved compared with direct-injection MS analysis, as they eluted earlier than the native lipids, owing to the decrease in hydrophobicity. In U937 and HL60 cells treated in vitro with t-butylhydroperoxide plus Fe2+, lipid oxidation could not be observed by direct injection, but LC-MS allowed the detection of monohydroperoxides of palmitoyl-linoleoyl and stearoyl-linoleoyl phosphatidylcholines. The levels of hydroperoxides observed in U937 cells were found to depend on the duration and severity of the oxidative stress. In cells treated with HOCl, chlorohydrins of palmitoyloleoyl phosphatidylcholine were observed by LC-MS. The method was able to detect very small amounts of oxidized lipids compared with the levels of native lipids present. The membrane-lipid profiles of these cells were found to be quite resistant to damage until high concentrations of oxidants were used. This is the first report of direct detection by LC-MS of intact oxidized phospholipids induced in cultured cells subjected to oxidative stress.

Interfacing low-energy SAW nebulization with liquid chromatography-mass spectrometry for the analysis of biological samples

Soft ionization methods for the introduction of labile biomolecules into a mass spectrometer are of fundamental importance to biomolecular analysis. Previously, electrospray ionization (ESI) and matrix assisted laser desorption-ionization (MALDI) have been the main ionization methods used. Surface acoustic wave nebulization (SAWN) is a new technique that has been demonstrated to deposit less energy into ions upon ion formation and transfer for detection than other methods for sample introduction into a mass spectrometer (MS). Here we report the optimization and use of SAWN as a nebulization technique for the introduction of samples from a low flow of liquid, and the interfacing of SAWN with liquid chromatographic separation (LC) for the analysis of a protein digest. This demonstrates that SAWN can be a viable, low-energy alternative to ESI for the LC-MS analysis of proteomic samples.

Detection of foveation windows and analysis of foveation sequences in congenital nystagmus

Congenital nystagmus (CN) is an ocular-motor disorder characterised by involuntary, conjugated ocular oscillations, that can arise since the first months of life. Pathogenesis of congenital nystagmus is still under investigation. In general, CN patients show a considerable decrease of their visual acuity: image fixation on the retina is disturbed by nystagmus continuous oscillations, mainly horizontal. However, image stabilisation is still achieved during the short periods in which eye velocity slows down while the target image is placed onto the fovea (called foveation intervals). To quantify the extent of nystagmus, eye movement recording are routinely employed, allowing physicians to extract and analyse nystagmus main features such as shape, amplitude and frequency. Using eye movement recording, it is also possible to compute estimated visual acuity predictors: analytical functions which estimates expected visual acuity using signal features such as foveation time and foveation position variability. Use of those functions add information to typical visual acuity measurement (e.g. Landolt C test) and could be a support for therapy planning or monitoring. This study focus on robust detection of CN patients' foveations. Specifically, it proposes a method to recognize the exact signal tracts in which a subject foveates, This paper also analyses foveation sequences. About 50 eyemovement recordings, either infrared-oculographic or electrooculographic, from different CN subjects were acquired. Results suggest that an exponential interpolation for the slow phases of nystagmus could improve foveation time computing and reduce influence of breaking saccades and data noise. Moreover a concise description of foveation sequence variability can be achieved using non-fitting splines. © 2009 Springer Berlin Heidelberg.

Synthesis and application of novel probes for the detection of cysteine sulphenic acids

Cysteine is a thiol containing amino acid that readily undergoes oxidation by reactive oxygen species (ROS) to form sulphenic (R-SOH) sulphinic (RSO2H) and sulphonic (RSO3H) acids. Thiol modifications of cysteine have been implicated as modulators of cellular processes and represent significant biological modifications that occur during oxidative stress and cell signalling. However, the different oxidation states are difficult to monitor in a physiological setting due to the limited availability of experimental tools. Therefore it is of interest to synthesise and use a chemical probe that selectively recognises the reversible oxidation state of cysteine sulphenic acid to understand more about oxidative signalling. The aim of this thesis was to investigate a synthetic approach for novel fluorescent probe synthesis, for the specific detection of cysteine sulphenic acids by fluorescence spectroscopy and confocal microscopy. N-[2-(Anthracen-2-ylamino)-2-oxoethyl]-3,5-dioxocyclohexanecarboxamide was synthesised in a multistep synthesis and characterised by nuclear magnetic resonance spectroscopy. The optimisation of conditions needed for sulphenic acid formation in a purified protein using human serum albumin (HSA) and the commercially available biotin tagged probe 3-(2,4-dioxocyclohexyl)propyl-5-((3aR,6S,6aS)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl)pentanoate (DCP-Bio1) were identified. This approach was extended to detect sulphenic acids in Jurkat T cells and CD4+ T cells pre- and post-stimulus. Buthionine sulfoximine (BSO) was used to manipulate the endogenous antioxidant glutathione (GSH) in human CD4+ T cells. Then the surface protein thiol levels and sulphenic acid formation was examined. T cells were also activated by the lectin phytohaemagglutinin-L (PHA-L) and formation of sulphenic acid was investigated using SDS-PAGE, western blotting and confocal microscopy. Resting Jurkat cells have two prominent protein bands that have sulphenic acid modifications whereas resting CD4+ T cells have an additional band present. When cells were treated with BSO the number of bands increased whereas activation reduced the number of proteins that were modified. The identities of the protein bands containing sulphenic acids were explored by mass spectrometry. Cysteine oxidation was observed in redox, metabolic and cytoskeletal proteins. In summary, a novel fluorescent probe for detection of cysteine sulphenic acids has been synthesised alongside a model system that introduces cysteine sulphenic acid in primary T cells. This probe has potential application in the subcellular localisation of cysteine oxidation during T cell signalling.

Detection and quantification of protein oxidation in sarcopenic models:a mass spectrometry study

Oxidised biomolecules in aged tissue could potentially be used as biomarkers for age-related diseases; however, it is still unclear whether they causatively contribute to ageing or are consequences of the ageing process. To assess the potential of using protein oxidation as markers of ageing, mass spectrometry (MS) was employed for the identification and quantification of oxidative modifications in obese (ob/ob) mice. Lean muscle mass and strength is reduced in obesity, representing a sarcopenic model in which the levels of oxidation can be evaluated for different muscular systems including calcium homeostasis, metabolism and contractility. Several oxidised residues were identified by tandem MS (MS/MS) in both muscle homogenate and isolated sarcoplasmic reticulum (SR), an organelle that regulates intracellular calcium levels in muscle. These modifications include oxidation of methionine, cysteine, tyrosine, and tryptophan in several proteins such as sarcoplasmic reticulum calcium ATPase (SERCA), glycogen phosphorylase, and myosin. Once modifications had been identified, multiple reaction monitoring MS (MRM) was used to quantify the percentage modification of oxidised residues within the samples. Preliminary data suggests proteins in ob/ob mice are more oxidised than the controls. For example SERCA, which constitutes 60-70% of the SR, had approximately a 2-fold increase in cysteine trioxidation of Cys561 in the obese model when compared to the control. Other obese muscle proteins have also shown a similar increase in oxidation for various residues. Further analysis with complex protein mixtures will determine the potential diagnostic use of MRM experiments for analysing protein oxidation in small biological samples such as muscle needle biopsies.

Optimisation of chromatographic separation of oxidised phospholipids and detection with targeted approaches provides greater coverage of the oxidised lipidome

Phospholipid oxidation by adventitious damage generates a wide variety of products with potentially novel biological activities that can modulate inflammatory processes associated with various diseases. To understand the biological importance of oxidised phospholipids (OxPL) and their potential role as disease biomarkers requires precise information about the abundance of these compounds in cells and tissues. There are many chemiluminescence and spectrophotometric assays available for detecting oxidised phospholipids, but they all have some limitations. Mass spectrometry coupled with liquid chromatography is a powerful and sensitive approach that can provide detailed information about the oxidative lipidome, but challenges still remain. The aim of this work is to develop improved methods for detection of OxPLs by optimisation of chromatographic separation through testing several reverse phase columns and solvent systems, and using targeted mass spectrometry approaches. Initial experiments were carried out using oxidation products generated in vitro to optimise the chromatography separation parameters and mass spectrometry parameters. We have evaluated the chromatographic separation of oxidised phosphatidylcholines (OxPCs) and oxidised phosphatidylethanolamines (OXPEs) using C8, C18 and C30 reverse phase, polystyrene – divinylbenzene based monolithic and mixed – mode hydrophilic interaction (HILIC) columns, interfaced with mass spectrometry. Our results suggest that the monolithic column was best able to separate short chain OxPCs and OxPEs from long chain oxidised and native PCs and PEs. However, variation in charge of polar head groups and extreme diversity of oxidised species make analysis of several classes of OxPLs within one analytical run impractical. We evaluated and optimised the chromatographic separation of OxPLs by serially coupling two columns: HILIC and monolith column that provided us the larger coverage of OxPL species in a single analytical run.

Variables affecting the collection and preservation of human scent components through instrumental and biological evaluations

In certain European countries and the United States of America, canines have been successfully used in human scent identification. There is however, limited scientific knowledge on the composition of human scent and the detection mechanism that produces an alert from canines. This lack of information has resulted in successful legal challenges to human scent evidence in the courts of law. ^ The main objective of this research was to utilize science to validate the current practices of using human scent evidence in criminal cases. The goals of this study were to utilize Headspace Solid Phase Micro Extraction Gas Chromatography Mass Spectrometry (HS-SPME-GC/MS) to determine the optimum collection and storage conditions for human scent samples, to investigate whether the amount of DNA deposited upon contact with an object affects the alerts produced by human scent identification canines, and to create a prototype pseudo human scent which could be used for training purposes. ^ Hand odor samples which were collected on different sorbent materials and exposed to various environmental conditions showed that human scent samples should be stored without prolonged exposure to UVA/UVB light to allow minimal changes to the overall scent profile. Various methods of collecting human scent from objects were also investigated and it was determined that passive collection methods yields ten times more VOCs by mass than active collection methods. ^ Through the use of polymerase chain reaction (PCR) no correlation was found between the amount of DNA that was deposited upon contact with an object and the alerts that were produced by human scent identification canines. Preliminary studies conducted to create a prototype pseudo human scent showed that it is possible to produce fractions of a human scent sample which can be presented to the canines to determine whether specific fractions or the entire sample is needed to produce alerts by the human scent identification canines. ^