Identification of blood lipid markers of docetaxel treatment in prostate cancer patients.

Docetaxel is commonly used for treatment of castration-resistant prostate cancer. Unfortunately, many prostate cancer patients develop resistance to docetaxel. Clinical markers less invasive than biopsies, such as blood samples, would be ideal for monitoring and predicting patient treatment outcomes to docetaxel.

Development of a semi-empirical physical model for transient NO emissions prediction from a high-speed diesel engine.

With emissions regulations becoming increasingly restrictive and the advent of real driving emissions limits, control of engine-out NO emissions remains an important research topic for diesel engines. Progress in experimental engine development and computational modelling has led to the generation of a large amount of high-fidelity emissions and in-cylinder data, making it attractive to use data-driven emissions prediction and control models. While pure data-driven methods have shown robustness in NO prediction during steady-state engine operation, deficiencies are found under transient operation and at engine conditions far outside the training range.

Impacts of daily household activities on indoor particulate and NO concentrations; a case study from oxford UK.

This study explores indoor air pollutant (PM, PM and NO) concentrations over a 15-week period during the COVID-19 pandemic in a typical suburban household in Oxford, UK. A multi-room intensive monitoring study was conducted in a single dwelling using 10 air quality sensors measuring real-time pollutant concentrations at 10 second intervals to assess temporal and spatial variability in PM, PM and NO concentrations, identify pollution-prone areas, and investigate the impact of residents' activities on indoor air quality. Significant spatial variations in PM concentrations were observed within the study dwelling, with highest hourly concentrations (769.

External Data Systems Enable Enhanced (and Sustainable) Fourier Transform Mass Spectrometry Imaging for Legacy Hybrid Linear Ion Trap-Orbitrap Platforms.

Legacy Fourier transform (FT) mass spectrometers provide robust platforms for bioanalytical mass spectrometry (MS) yet lack the most modern performance capabilities. For many laboratories, the routine investment in next generation instrumentation is cost prohibitive. Field-based upgrades provide a direct path to extend the usable lifespan of MS platforms which may be considered antiquated based on performance specifications at the time of manufacture.

Role of UDP-Glycosyltransferase () Genes in Detoxification and Glycosylation of 1-Hydroxyphenazine (1-HP) in .

is a useful model organism to study the xenobiotic detoxification pathways of various natural and synthetic toxins, but the mechanisms of phase II detoxification are understudied. 1-Hydroxyphenazine (1-HP), a toxin produced by the bacterium , kills . We previously showed that detoxifies 1-HP by adding one, two, or three glucose molecules in N2 worms.

Impacts of ambient air quality on acute asthma hospital admissions during the COVID-19 pandemic in Oxford City, UK: a time-series study.

Objectives: The study aims to investigate the short-term associations between exposure to ambient air pollution (nitrogen dioxide (NO), particulate matter pollution-particles with diameter<2.5 µm (PM) and PM) and incidence of asthma hospital admissions among adults, in Oxford, UK.

Design: Retrospective time-series study.

The impact of COVID-19 public health restrictions on particulate matter pollution measured by a validated low-cost sensor network in Oxford, UK.

Emergency responses to the COVID-19 pandemic led to major changes in travel behaviours and economic activities with arising impacts upon urban air quality. To date, these air quality changes associated with lockdown measures have typically been assessed using limited city-level regulatory monitoring data, however, low-cost air quality sensors provide capabilities to assess changes across multiple locations at higher spatial-temporal resolution, thereby generating insights relevant for future air quality interventions. The aim of this study was to utilise high-spatial resolution air quality information utilising data arising from a validated (using a random forest field calibration) network of 15 low-cost air quality sensors within Oxford, UK to monitor the impacts of multiple COVID-19 public heath restrictions upon particulate matter concentrations (PM, PM) from January 2020 to September 2021.

Microflow liquid chromatography - multi-emitter nanoelectrospray mass spectrometry of oligonucleotides.

While the most sensitive LC-MS methods for oligonucleotide analysis contain ion-pairs in the mobile phase, these modifiers have been associated with instrument contamination and ion suppression. Typically, entire LC-MS systems are reserved for oligonucleotide LC-MS when using ion-pairing buffers. To overcome these limitations, numerous HILIC methods, liberated from ion-pairs, have been recently developed.

On the pursuit of emissions-free clean mobility - Electric vehicles versus e-fuels.

With the passing of every second we get closer to a society that is more cognizant of the effect carbon dioxide emissions are having on our planet, and that is more willing to take part in sustainable efforts to combat this and ever more interested in investing in cleaner technologies like electric vehicles (EVs). EVs are marching strongly into a market that is currently dominated by internal combustion engine vehicles, the current main fuel of which is a known contributor to most of the emission related climate problems that we now find ourselves in. Moving ahead, it is important that any move from internal combustion engines to more nascent technologies like EVs is sustainable and not detrimental to the environment.

Unknown Metabolite Identification Using Machine Learning Collision Cross-Section Prediction and Tandem Mass Spectrometry.

Ion mobility (IM) spectrometry provides semiorthogonal data to mass spectrometry (MS), showing promise for identifying unknown metabolites in complex non-targeted metabolomics data sets. While current literature has showcased IM-MS for identifying unknowns under near ideal circumstances, less work has been conducted to evaluate the performance of this approach in metabolomics studies involving highly complex samples with difficult matrices. Here, we present a workflow incorporating molecular formula annotation and MS/MS structure elucidation using SIRIUS 4 with experimental IM collision cross-section (CCS) measurements and machine learning CCS predictions to identify differential unknown metabolites in mutant strains of .

An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics.

Untargeted metabolomics studies are unbiased but identifying the same feature across studies is complicated by environmental variation, batch effects, and instrument variability. Ideally, several studies that assay the same set of metabolic features would be used to select recurring features to pursue for identification. Here, we developed an anchored experimental design.

Impacts of emergency health protection measures upon air quality, traffic and public health: evidence from Oxford, UK.

Emergency responses to the COVID-19 pandemic led to major changes in travel behaviours and economic activities in 2020. Machine learning provides a reliable approach for assessing the contribution of these changes to air quality. This study investigates impacts of health protection measures upon air pollution and traffic emissions and estimates health and economic impacts arising from these changes during two national 'lockdown' periods in Oxford, UK.

The specificity of the malarial VAR2CSA protein for chondroitin sulfate depends on 4-O-sulfation and ligand accessibility.

Placental malaria infection is mediated by the binding of the malarial VAR2CSA protein to the placental glycosaminoglycan, chondroitin sulfate. Recombinant subfragments of VAR2CSA (rVAR2) have also been shown to bind specifically and with high affinity to cancer cells and tissues, suggesting the presence of a shared type of oncofetal chondroitin sulfate (ofCS) in the placenta and in tumors. However, the exact structure of ofCS and what determines the selective tropism of VAR2CSA remains poorly understood.

Comparison of High-Resolution Fourier Transform Mass Spectrometry Platforms for Putative Metabolite Annotation.

Fourier transform ion cyclotron resonance (FT-ICR) and Orbitrap mass spectrometry (MS) are among the highest-performing analytical platforms used in metabolomics. Non-targeted metabolomics experiments, however, yield extremely complex datasets that make metabolite annotation very challenging and sometimes impossible. The high-resolution accurate mass measurements of the leading MS platforms greatly facilitate this process by reducing mass errors and spectral overlaps.

Investigation of the Experimental Parameters of Ultraviolet Photodissociation for the Structural Characterization of Chondroitin Sulfate Glycosaminoglycan Isomers.

Glycosaminoglycans (GAGs) are linear polysaccharides that participate in a broad range of biological functions. Their incomplete biosynthesis pathway leads to nonuniform chains and complex mixtures. For this reason, the characterization of GAGs has been a difficult hurdle for the analytical community.

Online Capillary Zone Electrophoresis Negative Electron Transfer Dissociation Tandem Mass Spectrometry of Glycosaminoglycan Mixtures.

Glycosaminoglycans (GAGs) are important biological molecules that are highly anionic and occur in nature as complex mixtures. A platform that combines capillary zone electrophoresis (CZE) separations with mass spectrometry (MS) and gas-phase sequencing by using negative electron transfer dissociation (NETD) is shown to be efficacious for the structural analysis of GAG mixtures. CZE is a separation method well suited to the highly negatively charged nature of GAGs.

Structural Characterization of Glycosaminoglycan Carbohydrates Using Ultraviolet Photodissociation.

Structural characterization of sulfated glycosaminoglycans (GAGs) by mass spectrometry has long been a formidable analytical challenge owing to their high structural variability and the propensity for sulfate decomposition upon activation with low-energy ion activation methods. While derivatization and complexation workflows have aimed to generate informative spectra using low-energy ion activation methods, alternative ion activation methods present the opportunity to obtain informative spectra from native GAG structures. Both electron- and photon-based activation methods, including electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), and extreme ultraviolet photon activation, have been explored previously to overcome the limitations associated with low-energy activation methods for GAGs and other sulfated oligosaccharides.

Heparin/heparan sulfate analysis by covalently modified reverse polarity capillary zone electrophoresis-mass spectrometry.

Reverse polarity capillary zone electrophoresis coupled to negative ion mode mass spectrometry (CZE-MS) is shown to be an effective and sensitive tool for the analysis of glycosaminoglycan mixtures. Covalent modification of the inner wall of the separation capillary with neutral or cationic reagents produces a stable and durable surface that provides reproducible separations. By combining CZE-MS with a cation-coated capillary and a sheath flow interface, a rapid and reliable method has been developed for the analysis of sulfated oligosaccharides from dp4 to dp12.

An optical method for measuring exhaust gas pressure from an internal combustion engine at high speed.

Measurement of exhaust gas pressure at high speed in an engine is important for engine efficiency, computational fluid dynamics analysis, and turbocharger matching. Currently used piezoresistive sensors are bulky, require cooling, and have limited lifetimes. A new sensor system uses an interferometric technique to measure pressure by measuring the size of an optical cavity, which varies with pressure due to movement of a diaphragm.

Sequencing the Dermatan Sulfate Chain of Decorin.

Glycomics represents one of the last frontiers and most challenging in omic analysis. Glycosylation occurs in the endoplasmic reticulum and the Golgi organelle and its control is neither well-understood nor predictable based on proteomic or genomic analysis. One of the most structurally complex classes of glycoconjugates is the proteoglycans (PGs) and their glycosaminoglycan (GAG) side chains.

Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer.

The structural characterization of sulfated glycosaminoglycan (GAG) carbohydrates remains an important target for analytical chemists attributable to challenges introduced by the natural complexity of these mixtures and the defined need for molecular-level details to elucidate biological structure-function relationships. Tandem mass spectrometry has proven to be the most powerful technique for this purpose. Previously, electron detachment dissociation (EDD), in comparison to other methods of ion activation, has been shown to provide the largest number of useful cleavages for de novo sequencing of GAG oligosaccharides, but such experiments are restricted to Fourier transform ion cyclotron resonance mass spectrometers (FTICR-MS).

21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox.

We provide the initial performance evaluation of a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer operating at the Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory. The spectrometer constructed for the 21T system employs a commercial dual linear ion trap mass spectrometer coupled to a FTICR spectrometer designed and built in-house. Performance gains from moving to higher magnetic field strength are exemplified by the measurement of peptide isotopic fine structure, complex natural organic matter mixtures, and large proteins.

Analysis of heparin oligosaccharides by capillary electrophoresis-negative-ion electrospray ionization mass spectrometry.

Most hyphenated analytical approaches that rely on liquid chromatography-MS require relatively long separation times, produce incomplete resolution of oligosaccharide mixtures, use eluents that are incompatible with electrospray ionization, or require oligosaccharide derivatization. Here we demonstrate the analysis of heparin oligosaccharides, including disaccharides, ultralow molecular weight heparin, and a low molecular weight heparin, using a novel electrokinetic pump-based CE-MS coupling eletrospray ion source. Reverse polarity CE separation and negative-mode electrospray ionization were optimized using a volatile methanolic ammonium acetate electrolyte and sheath fluid.

An adaptable multiple power source for mass spectrometry and other scientific instruments.

An Adaptable Multiple Power Source (AMPS) system has been designed and constructed. The AMPS system can provide up to 16 direct current (DC) (±400 V; 5 mA), 4 radio frequency (RF) (two 500 VPP sinusoidal signals each, 0.5-5 MHz) channels, 2 high voltage sources (±6 kV), and one ∼40 W, 250 °C temperature-regulated heater.

Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer.

Enhancements to the ion source and transfer optics of our 9.4 T Fourier transform ion cyclotron resonance (ICR) mass spectrometer have resulted in improved ion transmission efficiency for more sensitive mass measurement of complex mixtures at the MS and MS/MS levels. The tube lens/skimmer has been replaced by a dual ion funnel and the following octopole by a quadrupole for reduced ion cloud radial expansion before transmission into a mass-selective quadrupole.