subject:(Mass spectrometry Data processing)

University of Dundee

1. Ahmad, Yasmeen. Management, visualisation & mining of quantitative proteomics data.

Degree: PhD, 2012, University of Dundee

URL: http://hdl.handle.net/10588/6ed071fc-e43b-410c-898d-50529dc298ce

► Exponential data growth in life sciences demands cross discipline work that brings together computing and life sciences in a usable manner that can enhance knowledge… (more)

▼ Exponential data growth in life sciences demands cross discipline work that brings together computing and life sciences in a usable manner that can enhance knowledge and understanding in both fields. High throughput approaches, advances in instrumentation and overall complexity of mass spectrometry data have made it impossible for researchers to manually analyse data using existing market tools. By applying a user-centred approach to effectively capture domain knowledge and experience of biologists, this thesis has bridged the gap between computation and biology through software, PepTracker (http://www.peptracker.com). This software provides a framework for the systematic detection and analysis of proteins that can be correlated with biological properties to expand the functional annotation of the genome. The tools created in this study aim to place analysis capabilities back in the hands of biologists, who are expert in evaluating their data. Another major advantage of the PepTracker suite is the implementation of a data warehouse, which manages and collates highly annotated experimental data from numerous experiments carried out by many researchers. This repository captures the collective experience of a laboratory, which can be accessed via user-friendly interfaces. Rather than viewing datasets as isolated components, this thesis explores the potential that can be gained from collating datasets in a “super-experiment” ideology, leading to formation of broad ranging questions and promoting biology driven lines of questioning. This has been uniquely implemented by integrating tools and techniques from the field of Business Intelligence with Life Sciences and successfully shown to aid in the analysis of proteomic interaction experiments. Having conquered a means of documenting a static proteomics snapshot of cells, the proteomics field is progressing towards understanding the extremely complex nature of cell dynamics. PepTracker facilitates this by providing the means to gather and analyse many protein properties to generate new biological insight, as demonstrated by the identification of novel protein isoforms.

Subjects/Keywords: Mass Spectrometry; Proteomics; Data Management; Visualisation; Data Mining; Business Intelligence; Analytics; Data Science

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ahmad, Y. (2012). Management, visualisation & mining of quantitative proteomics data. (Doctoral Dissertation). University of Dundee. Retrieved from http://hdl.handle.net/10588/6ed071fc-e43b-410c-898d-50529dc298ce

Chicago Manual of Style (16^th Edition):

Ahmad, Yasmeen. “Management, visualisation & mining of quantitative proteomics data.” 2012. Doctoral Dissertation, University of Dundee. Accessed December 09, 2019. http://hdl.handle.net/10588/6ed071fc-e43b-410c-898d-50529dc298ce.

MLA Handbook (7^th Edition):

Ahmad, Yasmeen. “Management, visualisation & mining of quantitative proteomics data.” 2012. Web. 09 Dec 2019.

Vancouver:

Ahmad Y. Management, visualisation & mining of quantitative proteomics data. [Internet] [Doctoral dissertation]. University of Dundee; 2012. [cited 2019 Dec 09]. Available from: http://hdl.handle.net/10588/6ed071fc-e43b-410c-898d-50529dc298ce.

Council of Science Editors:

Ahmad Y. Management, visualisation & mining of quantitative proteomics data. [Doctoral Dissertation]. University of Dundee; 2012. Available from: http://hdl.handle.net/10588/6ed071fc-e43b-410c-898d-50529dc298ce

University of Dundee

2. Ahmad, Yasmeen. Management, visualisation & mining of quantitative proteomics data.

Degree: PhD, 2012, University of Dundee

URL: https://discovery.dundee.ac.uk/en/studentTheses/6ed071fc-e43b-410c-898d-50529dc298ce ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578847

► Exponential data growth in life sciences demands cross discipline work that brings together computing and life sciences in a usable manner that can enhance knowledge… (more)

▼ Exponential data growth in life sciences demands cross discipline work that brings together computing and life sciences in a usable manner that can enhance knowledge and understanding in both fields. High throughput approaches, advances in instrumentation and overall complexity of mass spectrometry data have made it impossible for researchers to manually analyse data using existing market tools. By applying a user-centred approach to effectively capture domain knowledge and experience of biologists, this thesis has bridged the gap between computation and biology through software, PepTracker (http://www.peptracker.com). This software provides a framework for the systematic detection and analysis of proteins that can be correlated with biological properties to expand the functional annotation of the genome. The tools created in this study aim to place analysis capabilities back in the hands of biologists, who are expert in evaluating their data. Another major advantage of the PepTracker suite is the implementation of a data warehouse, which manages and collates highly annotated experimental data from numerous experiments carried out by many researchers. This repository captures the collective experience of a laboratory, which can be accessed via user-friendly interfaces. Rather than viewing datasets as isolated components, this thesis explores the potential that can be gained from collating datasets in a “super-experiment” ideology, leading to formation of broad ranging questions and promoting biology driven lines of questioning. This has been uniquely implemented by integrating tools and techniques from the field of Business Intelligence with Life Sciences and successfully shown to aid in the analysis of proteomic interaction experiments. Having conquered a means of documenting a static proteomics snapshot of cells, the proteomics field is progressing towards understanding the extremely complex nature of cell dynamics. PepTracker facilitates this by providing the means to gather and analyse many protein properties to generate new biological insight, as demonstrated by the identification of novel protein isoforms.

Subjects/Keywords: 572; Mass Spectrometry; Proteomics; Data Management; Visualisation; Data Mining; Business Intelligence; Analytics; Data Science

Record Details Similar Records Cite « Share

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ahmad, Y. (2012). Management, visualisation & mining of quantitative proteomics data. (Doctoral Dissertation). University of Dundee. Retrieved from https://discovery.dundee.ac.uk/en/studentTheses/6ed071fc-e43b-410c-898d-50529dc298ce ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578847

Chicago Manual of Style (16^th Edition):

Ahmad, Yasmeen. “Management, visualisation & mining of quantitative proteomics data.” 2012. Doctoral Dissertation, University of Dundee. Accessed December 09, 2019. https://discovery.dundee.ac.uk/en/studentTheses/6ed071fc-e43b-410c-898d-50529dc298ce ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578847.

MLA Handbook (7^th Edition):

Ahmad, Yasmeen. “Management, visualisation & mining of quantitative proteomics data.” 2012. Web. 09 Dec 2019.

Vancouver:

Ahmad Y. Management, visualisation & mining of quantitative proteomics data. [Internet] [Doctoral dissertation]. University of Dundee; 2012. [cited 2019 Dec 09]. Available from: https://discovery.dundee.ac.uk/en/studentTheses/6ed071fc-e43b-410c-898d-50529dc298ce ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578847.

Council of Science Editors:

Ahmad Y. Management, visualisation & mining of quantitative proteomics data. [Doctoral Dissertation]. University of Dundee; 2012. Available from: https://discovery.dundee.ac.uk/en/studentTheses/6ed071fc-e43b-410c-898d-50529dc298ce ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578847

University of Manchester

3. Sayers, Rebekah. Proteomic profiling of processing-induced modifications to food proteins.

Degree: 2017, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308813

► Peanut allergy typically results from sensitisation to one or more integral seed storage proteins; Ara h 1, 3 or 2/6. Reactions can be triggered by… (more)

▼ Peanut allergy typically results from sensitisation to one or more integral seed storage proteins; Ara h 1, 3 or 2/6. Reactions can be triggered by as little as 3 mg protein in 10% of allergic individuals and are often severe, inducing anaphylaxis which can be fatal. Accidental exposure through unintended presence can therefore be hazardous and foods must be labelled appropriately. Thermal processing is one of the main factors affecting protein properties in food systems, including the formation of Maillard reaction products. Research has suggested a link between the allergenicity of foods and cooking methods employed. A systematic study was undertaken to assess the thermal dependence of these hazard proteins, focusing on changes to solubility and chemical modifications which may alter IgE binding. Proteomic profiling was used to assess the allergenic content of peanut products and develop alternative methods for allergen analysis to support evidence-based application of precautionary allergen labelling. Runner variety peanuts were processed (boiled, fried, roasted) and their protein content determined. Proteins extracts were characterised by 1D- and 2D-polyacrylamide gel electrophoresis, including differential in-gel electrophoresis. Proteomic profiling was undertaken using label-free analysis to assess allergen composition and investigate the formation of Maillard reaction products on the most clinically relevant proteins. Peanut allergen peptide targets were then identified and used to develop label-based quantitation methods and applied to (i) investigate effects of processing on peptide targets and (ii) determine peanut in chocolate products in comparison with a commercial ELISA kit. Orthogonal studies were performed using serum samples from peanut allergic patients obtained from the Manchester Respiratory, Allergy and Thoracic Surgery (ManARTS) Biobank. Patient IgE reactivity to peanut and processed peanut products was assessed by immunoblotting, inhibition ELISA and mediator release assays.Protein solubility was reduced by thermal processing and processed protein required harsh denaturing conditions for extraction. Qualitative analysis highlighted decreased solubility of key allergens, modifications and aggregation after heating. Proteomic profiling identified and quantified different isoforms of the major peanut allergens. The protein content of processed peanuts was reduced by boiling, specifically the 2S albumins, which transferred into the cooking water. The performance of peptides selected for targeted MRM experiments was influenced by thermal processing and the presence of cocoa phenolics. Ara h 2 peptides flanked by arginine were thermostable and may prove more reliable for quantification. Application of microfluidic separation enhanced the efficiency of target ionisation in complex matrices acquiring important sensitivity gains. Maillard modifications to clinically relevant proteins Ara h 2/6 were found within IgE binding domains in raw and processed peanuts. IgE reactivity studies confirmed reduced… Advisors/Committee Members: BARRAN, PERDITA P, Barran, Perdita, Mills, Clare.

Subjects/Keywords: Food allergy; Mass spectrometry; Thermal processing; Proteomics; Allergen; Peanut; Immunotherapy

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sayers, R. (2017). Proteomic profiling of processing-induced modifications to food proteins. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308813

Chicago Manual of Style (16^th Edition):

Sayers, Rebekah. “Proteomic profiling of processing-induced modifications to food proteins.” 2017. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308813.

MLA Handbook (7^th Edition):

Sayers, Rebekah. “Proteomic profiling of processing-induced modifications to food proteins.” 2017. Web. 09 Dec 2019.

Vancouver:

Sayers R. Proteomic profiling of processing-induced modifications to food proteins. [Internet] [Doctoral dissertation]. University of Manchester; 2017. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308813.

Council of Science Editors:

Sayers R. Proteomic profiling of processing-induced modifications to food proteins. [Doctoral Dissertation]. University of Manchester; 2017. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308813

University of Manchester

4. Sayers, Rebekah. Proteomic profiling of processing-induced modifications to food proteins.

Degree: PhD, 2017, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/proteomic-profiling-of-processinginduced-modifications-to-food-proteins(f6560c3b-4f80-49b9-94c2-6cd9b41288fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764552

► Peanut allergy typically results from sensitisation to one or more integral seed storage proteins; Ara h 1, 3 or 2/6. Reactions can be triggered by… (more)

▼ Peanut allergy typically results from sensitisation to one or more integral seed storage proteins; Ara h 1, 3 or 2/6. Reactions can be triggered by as little as 3 mg protein in 10% of allergic individuals and are often severe, inducing anaphylaxis which can be fatal. Accidental exposure through unintended presence can therefore be hazardous and foods must be labelled appropriately. Thermal processing is one of the main factors affecting protein properties in food systems, including the formation of Maillard reaction products. Research has suggested a link between the allergenicity of foods and cooking methods employed. A systematic study was undertaken to assess the thermal dependence of these hazard proteins, focusing on changes to solubility and chemical modifications which may alter IgE binding. Proteomic profiling was used to assess the allergenic content of peanut products and develop alternative methods for allergen analysis to support evidence-based application of precautionary allergen labelling. Runner variety peanuts were processed (boiled, fried, roasted) and their protein content determined. Proteins extracts were characterised by 1D- and 2D-polyacrylamide gel electrophoresis, including differential in-gel electrophoresis. Proteomic profiling was undertaken using label-free analysis to assess allergen composition and investigate the formation of Maillard reaction products on the most clinically relevant proteins. Peanut allergen peptide targets were then identified and used to develop label-based quantitation methods and applied to (i) investigate effects of processing on peptide targets and (ii) determine peanut in chocolate products in comparison with a commercial ELISA kit. Orthogonal studies were performed using serum samples from peanut allergic patients obtained from the Manchester Respiratory, Allergy and Thoracic Surgery (ManARTS) Biobank. Patient IgE reactivity to peanut and processed peanut products was assessed by immunoblotting, inhibition ELISA and mediator release assays. Protein solubility was reduced by thermal processing and processed protein required harsh denaturing conditions for extraction. Qualitative analysis highlighted decreased solubility of key allergens, modifications and aggregation after heating. Proteomic profiling identified and quantified different isoforms of the major peanut allergens. The protein content of processed peanuts was reduced by boiling, specifically the 2S albumins, which transferred into the cooking water. The performance of peptides selected for targeted MRM experiments was influenced by thermal processing and the presence of cocoa phenolics. Ara h 2 peptides flanked by arginine were thermostable and may prove more reliable for quantification. Application of microfluidic separation enhanced the efficiency of target ionisation in complex matrices acquiring important sensitivity gains. Maillard modifications to clinically relevant proteins Ara h 2/6 were found within IgE binding domains in raw and processed peanuts. IgE reactivity studies confirmed reduced…

Subjects/Keywords: Allergen; Proteomics; Food allergy; Mass spectrometry; Peanut; Thermal processing; Immunotherapy

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sayers, R. (2017). Proteomic profiling of processing-induced modifications to food proteins. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/proteomic-profiling-of-processinginduced-modifications-to-food-proteins(f6560c3b-4f80-49b9-94c2-6cd9b41288fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764552

Chicago Manual of Style (16^th Edition):

Sayers, Rebekah. “Proteomic profiling of processing-induced modifications to food proteins.” 2017. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/proteomic-profiling-of-processinginduced-modifications-to-food-proteins(f6560c3b-4f80-49b9-94c2-6cd9b41288fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764552.

MLA Handbook (7^th Edition):

Sayers, Rebekah. “Proteomic profiling of processing-induced modifications to food proteins.” 2017. Web. 09 Dec 2019.

Vancouver:

Sayers R. Proteomic profiling of processing-induced modifications to food proteins. [Internet] [Doctoral dissertation]. University of Manchester; 2017. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/proteomic-profiling-of-processinginduced-modifications-to-food-proteins(f6560c3b-4f80-49b9-94c2-6cd9b41288fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764552.

Council of Science Editors:

Sayers R. Proteomic profiling of processing-induced modifications to food proteins. [Doctoral Dissertation]. University of Manchester; 2017. Available from: https://www.research.manchester.ac.uk/portal/en/theses/proteomic-profiling-of-processinginduced-modifications-to-food-proteins(f6560c3b-4f80-49b9-94c2-6cd9b41288fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764552

University of Manchester

5. Reamtong, Onrapak. The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide.

Degree: 2010, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:86719

► (2R)-N-Benzyl-2-acetamido-3-methoxypropionamide (lacosamide) is ananticonvulsant (Choi et al., 1996); under the brand name “Vimpat” this small molecule hasrecently been approved by the European Medicines Agency and… (more)

▼ (2R)-N-Benzyl-2-acetamido-3-methoxypropionamide (lacosamide) is ananticonvulsant (Choi et al., 1996); under the brand name “Vimpat” this small molecule hasrecently been approved by the European Medicines Agency and the U.S. Food and DrugAdministration for the treatment of epilepsy. The purpose of the research reported here is todevelop and apply mass spectrometry approaches to the determination of protein targets ofthis novel therapeutic.The general strategy involves selecting potential target proteins using lacosamideanalogues incorporating an ‘affinity bait’ to enable covalent modification binding to targetproteins, and a ‘chemical reporter’ for the selective recovery of modified proteins.Lacosamide analogues are incubated with biological samples (primarily mouse brainextracts) and the modified proteins are recovered by introduction of a biotin tag (via thechemical reporter group). Streptavidin affinity chromatography is then used to enrich forbound molecules. The enriched proteins are subjected to tryptic digestion and the resultantpeptides analysed by reversed phase liquid chromatography coupled with tandem MS,enabling recognition of proteins via database searchingFirstly, mass spectrometric characterisation of the biotinyl (R)-lacosamide analoguebound to model compounds was performed. Adducts with protected lysine, neurotensin andenolase were analysed. The data showed that ESI was more suitable for ionisation ofmodified peptides and proteins than MALDI. The biotin enrichment strategy was applied tomouse brain lysate to identify putative candidate target proteins. Twenty-eight candidatetarget proteins were identified. Moreover, the 14-3-3 protein family, CRMP2 and thesodium/potassium-transporting ATPase family showed preference for the biologically active(R)- isomer over the (S)- lacosamide analogue using a fluorescence tag.Three more biotinyl lacosamide analogues containing different affinity baits wereused to enrich candidate target proteins of lacosamide. Most of the identified target proteinssupported the findings of the analogue A. To indicate the binding sites, a method wasdeveloped for enriching peptides modified by the biotinyl (R)-lacosamide analogue, usingstreptavidin beads and subsequently analysed these biotinylated peptides using CID andETD fragmentation methods. Neither fragmentation technique was optimal for elucidation ofthe sequence or site of modification of unknown target peptides. Purified recombinantproteins were therefore adducted with an AB-(R)-lacosamide analogue lacking the biotinprobe. This smaller (R)-lacosamide analogue underwent less fragmentation than the biotinanalogue during CID and could be used for sequence and site identification of the modifiedpeptides.In summary, the studies illustrated the power of MS to study drug mechanisms viathe discovery of candidate protein targets. Advisors/Committee Members: EYERS, CLAIRE CE, Gaskell, Simon, Eyers, Claire.

Subjects/Keywords: Mass spectrometry; lacosamide

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Reamtong, O. (2010). The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:86719

Chicago Manual of Style (16^th Edition):

Reamtong, Onrapak. “The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide.” 2010. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:86719.

MLA Handbook (7^th Edition):

Reamtong, Onrapak. “The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide.” 2010. Web. 09 Dec 2019.

Vancouver:

Reamtong O. The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide. [Internet] [Doctoral dissertation]. University of Manchester; 2010. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:86719.

Council of Science Editors:

Reamtong O. The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide. [Doctoral Dissertation]. University of Manchester; 2010. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:86719

University of Manchester

6. Couto, Narciso Alves Da silva. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach.

Degree: 2011, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515

► The main work presented in this thesis describes proteomics strategies applied to study the trafficking and turnover of glutathione reductase (Glr1) isoforms in the cytosol… (more)

▼ The main work presented in this thesis describes proteomics strategies applied to study the trafficking and turnover of glutathione reductase (Glr1) isoforms in the cytosol and mitochondria of Saccharomyces cerevisiae. Additional work was performed in order to understand mass spectrometric response factors and how they can affect peptides representation in the mass spectra. The opportunity to study two sub proteomes involved in biofilm formation of Pseudomonas aeruginosa PAO1 arose during my PhD and their analysis is also presented.Glr1 is a low abundant protein involved in the defence mechanisms against reactive oxygen species, which are sources of many diseases. Because of its biological relevance, considerable effort has been made in order to understand its functional role in the cell. This protein has been studied using biochemical strategies. In yeast, the cytosolic and mitochondrial forms of glutathione reductase are expressed by the same gene, GLR1, using alternative start codons. Translation from the first AUG codon generates the mitochondrial form incorporating a transit peptide necessary for import into the mitochondria. If the translation starts at the second AUG codon, the cytosolic counterpart is generated. Biochemical approaches show that the first AUG codon is not in favourable context and it has been suggested that leaky scanning accounts for the abundance of the cytosolic protein.The analysis of Glr1 forms by mass spectrometry was demanded because only the N-terminal region is informative about similarities and differences between cytosolic and mitochondrial forms. The protein is also of low abundance in both cytosol and mitochondrial compartments. A genetically modified strain, over-expressing this protein was, therefore, used throughout this work in order to analyse glutathione reductase in the mitochondria. This was not possible with the wild-type strain.Because the first AUG codon is now in context, the over-producing strain (MORF) yields both cytosolic and full length mitochondrial isoforms in the cytosol. Analysis of the mitochondrial protein shows that the cleavage of the pre-sequence is not specific. Three different forms of the mitochondrial N-terminal peptide were detected. Some attention was also devoted to glutathione reductase turnover in both cytosol and mitochondrial compartments using the genetically modified strain. Both N-terminal peptides generated from translation starting in the first and second AUG codon as well as mid-chain peptides from the cytosol fraction and one mid-chain peptide from the mitochondrial fraction, were used to calculate relative turnover measurements. My results illustrate that the mitochondrial protein is in faster turnover than the cytosolic counterpart. Moreover, the long and short forms observed in the cytosol also show slightly different turnover rates, the long form presenting faster turnover than the short form. Rapid turnover therefore maintains the level of glutathione reductase in the mitochondria.Despite the exquisite sensitivity of mass… Advisors/Committee Members: GASKELL, SIMON SJ, EYERS, CLAIRE CE, GORRY, PETER PA, BARBER, JILL JA, Gaskell, Simon, Gaskell, Simon, Eyers, Claire, Gorry, Peter, Barber, Jill, Barber, Jill.

Subjects/Keywords: Proteomics; Mass Spectrometry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Couto, N. A. D. s. (2011). Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515

Chicago Manual of Style (16^th Edition):

Couto, Narciso Alves Da silva. “Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach.” 2011. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515.

MLA Handbook (7^th Edition):

Couto, Narciso Alves Da silva. “Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach.” 2011. Web. 09 Dec 2019.

Vancouver:

Couto NADs. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach. [Internet] [Doctoral dissertation]. University of Manchester; 2011. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515.

Council of Science Editors:

Couto NADs. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach. [Doctoral Dissertation]. University of Manchester; 2011. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515

University of Oxford

7. Hauschild, Jennifer M. Fourier transform ion cyclotron resonance mass spectrometry for petroleomics.

Degree: 2012, University of Oxford

URL: http://ora.ox.ac.uk/objects/uuid:8604a373-fb6b-4bc0-8dc1-464a191b1fac ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555369

► The past two decades have witnessed tremendous advances in the field of high accuracy, high mass resolution data acquisition of complex samples such as crude… (more)

▼ The past two decades have witnessed tremendous advances in the field of high accuracy, high mass resolution data acquisition of complex samples such as crude oils and the human proteome. With the development of Fourier transform ion cyclotron resonance mass spectrometry, the rapidly growing field of petroleomics has emerged, whose goal is to process and analyse the large volumes of complex and often poorly understood data on crude oils generated by mass spectrometry. As global oil resources deplete, oil companies are increasingly moving towards the extraction and refining of the still plentiful reserves of heavy, carbon rich and highly contaminated crude oil. It is essential that the oil industry gather the maximum possible amount of information about the crude oil prior to setting up the drilling infrastructure, in order to reduce processing costs. This project describes how machine learning can be used as a novel way to extract critical information from complex mass spectra which will aid in the processing of crude oils. The thesis discusses the experimental methods involved in acquiring high accuracy mass spectral data for a large and key industry-standard set of crude oil samples. These data are subsequently analysed to identify possible links between the raw mass spectra and certain physical properties of the oils, such as pour point and sulphur content. Methods including artificial neural networks and self organising maps are described and the use of spectral clustering and pattern recognition to classify crude oils is investigated. The main focus of the research, the creation of an original simulated annealing genetic algorithm hybrid technique (SAGA), is discussed in detail and the successes of modelling a number of different datasets using all described methods are outlined. Despite the complexity of the underlying mass spectrometry data, which reflects the considerable chemical diversity of the samples themselves, the results show that physical properties can be modelled with varying degrees of success. When modelling pour point temperatures, the artificial neural network achieved an average prediction error of less than 10% while SAGA predicted the same values with an average accuracy of more than 85%. It did not prove possible to model any of the other properties with such statistical significance; however improvements to feature extraction and pre-processing of the spectral data as well as enhancement of the modelling techniques should yield more consistent and statistically reliable results. These should in due course lead to a comprehensive model which the oil industry can use to process crude oil data using rapid and cost effective analytical methods.

Subjects/Keywords: 547.83; Physical Sciences : Chemistry & allied sciences : Computational chemistry : Mass spectrometry : Physical & theoretical chemistry : mass spectrometry : machine learning : petroleomics : artificial neural networks : data modelling : genetic algorithms

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hauschild, J. M. (2012). Fourier transform ion cyclotron resonance mass spectrometry for petroleomics. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:8604a373-fb6b-4bc0-8dc1-464a191b1fac ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555369

Chicago Manual of Style (16^th Edition):

Hauschild, Jennifer M. “Fourier transform ion cyclotron resonance mass spectrometry for petroleomics.” 2012. Doctoral Dissertation, University of Oxford. Accessed December 09, 2019. http://ora.ox.ac.uk/objects/uuid:8604a373-fb6b-4bc0-8dc1-464a191b1fac ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555369.

MLA Handbook (7^th Edition):

Hauschild, Jennifer M. “Fourier transform ion cyclotron resonance mass spectrometry for petroleomics.” 2012. Web. 09 Dec 2019.

Vancouver:

Hauschild JM. Fourier transform ion cyclotron resonance mass spectrometry for petroleomics. [Internet] [Doctoral dissertation]. University of Oxford; 2012. [cited 2019 Dec 09]. Available from: http://ora.ox.ac.uk/objects/uuid:8604a373-fb6b-4bc0-8dc1-464a191b1fac ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555369.

Council of Science Editors:

Hauschild JM. Fourier transform ion cyclotron resonance mass spectrometry for petroleomics. [Doctoral Dissertation]. University of Oxford; 2012. Available from: http://ora.ox.ac.uk/objects/uuid:8604a373-fb6b-4bc0-8dc1-464a191b1fac ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555369

8. Gray, Christopher. Comprehensive stereochemical sequencing of carbohydrates and characterisation oftheir binding partners using hyphenated mass spectrometry methods.

Degree: 2017, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307280

► Glycans and their conjugates form the largest and most diverse class of biologicalmolecules found within nature. These glycosides are vital for numerous cellular functionsincluding recognition… (more)

▼ Glycans and their conjugates form the largest and most diverse class of biologicalmolecules found within nature. These glycosides are vital for numerous cellular functionsincluding recognition events, protein stabilisation and energy storage, to name a few.Additionally, abnormalities within these structures are associated with a wide range ofdisease states. As a result, robust analytical techniques capable of in depth characterisationof carbohydrates and their binding partners are required. Currently, liquid chromatographycoupled with tandem mass spectrometry (MS2) is the ‘gold standard’ for characterisingthese species. However there are inherent challenges for ‘sequencing’ carbohydrates giventhat most structures are diastereomeric. As a result MS alone is insufficient to fullyelucidate all stereochemical and often regiochemical information and alternative analyticaltechniques have inherent issues meaning that they are not suitable for medium/highthroughputanalysis. To facilitate elucidation of these structures, ion mobility spectrometry(IMS) has been used in-line with MS2. IMS of mono- and di-saccharide product ionsgenerate by collision-induced dissociation (CID) of various glycans and their conjugatesenables unambiguous identification of the monomer and the regio-/stereo-chemistry of theglycosidic bond, independent of the precursor structure.Also, given the prominence of glycans in biological recognition events, high-throughputtechniques capable of elucidating and characterising carbohydrate to glycan-bindingprotein (GBP) interactions are highly sought after. Historically, (micro)array strategies areemployed to screen large numbers of biological interactions, with detection conventionallyachieved with fluorescent tagging. The major disadvantage of this approach is therequirement of a labelling step to facilitate detection of glycan-GBP binding. MS offers theability to unambiguously identify GBPs when combined with routine bottom-upproteomics strategies, namely on-chip proteolysis followed by mass fingerprinting andMS2 analysis and subsequent comparison to protein databases.It is anticipated that these methodologies developed throughout these studies, both forcarbohydrate sequencing and the characterisation of glycan-binding proteins, will greatlyadd to the Glycomics toolbox. Advisors/Committee Members: EYERS, CLAIRE CE, Flitsch, Sabine, Eyers, Claire.

Subjects/Keywords: Mass Spectrometry Ion mobility spectrometry Glycans Arrays

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APA (6^th Edition):

Gray, C. (2017). Comprehensive stereochemical sequencing of carbohydrates and characterisation oftheir binding partners using hyphenated mass spectrometry methods. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307280

Chicago Manual of Style (16^th Edition):

Gray, Christopher. “Comprehensive stereochemical sequencing of carbohydrates and characterisation oftheir binding partners using hyphenated mass spectrometry methods.” 2017. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307280.

MLA Handbook (7^th Edition):

Gray, Christopher. “Comprehensive stereochemical sequencing of carbohydrates and characterisation oftheir binding partners using hyphenated mass spectrometry methods.” 2017. Web. 09 Dec 2019.

Vancouver:

Gray C. Comprehensive stereochemical sequencing of carbohydrates and characterisation oftheir binding partners using hyphenated mass spectrometry methods. [Internet] [Doctoral dissertation]. University of Manchester; 2017. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307280.

Council of Science Editors:

Gray C. Comprehensive stereochemical sequencing of carbohydrates and characterisation oftheir binding partners using hyphenated mass spectrometry methods. [Doctoral Dissertation]. University of Manchester; 2017. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307280

University of Manchester

9. Couto, Narciso Alves Da silva. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae : a proteomic approach.

Degree: PhD, 2011, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/partition-and-turnover-of-glutathione-reductase-in-saccharomyces-cerevisiae-a-proteomic-approach(5f813b0d-4742-4f7a-b4bd-a4e309e9e68c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686711

► The main work presented in this thesis describes proteomics strategies applied to study the trafficking and turnover of glutathione reductase (Glr1) isoforms in the cytosol… (more)

▼ The main work presented in this thesis describes proteomics strategies applied to study the trafficking and turnover of glutathione reductase (Glr1) isoforms in the cytosol and mitochondria of Saccharomyces cerevisiae. Additional work was performed in order to understand mass spectrometric response factors and how they can affect peptides representation in the mass spectra. The opportunity to study two sub proteomes involved in biofilm formation of Pseudomonas aeruginosa PAO1 arose during my PhD and their analysis is also presented. Glr1 is a low abundant protein involved in the defence mechanisms against reactive oxygen species, which are sources of many diseases. Because of its biological relevance, considerable effort has been made in order to understand its functional role in the cell. This protein has been studied using biochemical strategies. In yeast, the cytosolic and mitochondrial forms of glutathione reductase are expressed by the same gene, GLR1, using alternative start codons. Translation from the first AUG codon generates the mitochondrial form incorporating a transit peptide necessary for import into the mitochondria. If the translation starts at the second AUG codon, the cytosolic counterpart is generated. Biochemical approaches show that the first AUG codon is not in favourable context and it has been suggested that leaky scanning accounts for the abundance of the cytosolic protein. The analysis of Glr1 forms by mass spectrometry was demanded because only the N-terminal region is informative about similarities and differences between cytosolic and mitochondrial forms. The protein is also of low abundance in both cytosol and mitochondrial compartments. A genetically modified strain, over-expressing this protein was, therefore, used throughout this work in order to analyse glutathione reductase in the mitochondria. This was not possible with the wild-type strain. Because the first AUG codon is now in context, the over-producing strain (MORF) yields both cytosolic and full length mitochondrial isoforms in the cytosol. Analysis of the mitochondrial protein shows that the cleavage of the pre-sequence is not specific. Three different forms of the mitochondrial N-terminal peptide were detected. Some attention was also devoted to glutathione reductase turnover in both cytosol and mitochondrial compartments using the genetically modified strain. Both N-terminal peptides generated from translation starting in the first and second AUG codon as well as mid-chain peptides from the cytosol fraction and one mid-chain peptide from the mitochondrial fraction, were used to calculate relative turnover measurements. My results illustrate that the mitochondrial protein is in faster turnover than the cytosolic counterpart. Moreover, the long and short forms observed in the cytosol also show slightly different turnover rates, the long form presenting faster turnover than the short form. Rapid turnover therefore maintains the level of glutathione reductase in the mitochondria. Despite the exquisite sensitivity of mass…

Subjects/Keywords: 572; Proteomics; Mass Spectrometry

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APA (6^th Edition):

Couto, N. A. D. s. (2011). Partition and turnover of glutathione reductase in Saccharomyces cerevisiae : a proteomic approach. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/partition-and-turnover-of-glutathione-reductase-in-saccharomyces-cerevisiae-a-proteomic-approach(5f813b0d-4742-4f7a-b4bd-a4e309e9e68c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686711

Chicago Manual of Style (16^th Edition):

Couto, Narciso Alves Da silva. “Partition and turnover of glutathione reductase in Saccharomyces cerevisiae : a proteomic approach.” 2011. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/partition-and-turnover-of-glutathione-reductase-in-saccharomyces-cerevisiae-a-proteomic-approach(5f813b0d-4742-4f7a-b4bd-a4e309e9e68c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686711.

MLA Handbook (7^th Edition):

Couto, Narciso Alves Da silva. “Partition and turnover of glutathione reductase in Saccharomyces cerevisiae : a proteomic approach.” 2011. Web. 09 Dec 2019.

Vancouver:

Couto NADs. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae : a proteomic approach. [Internet] [Doctoral dissertation]. University of Manchester; 2011. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/partition-and-turnover-of-glutathione-reductase-in-saccharomyces-cerevisiae-a-proteomic-approach(5f813b0d-4742-4f7a-b4bd-a4e309e9e68c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686711.

Council of Science Editors:

Couto NADs. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae : a proteomic approach. [Doctoral Dissertation]. University of Manchester; 2011. Available from: https://www.research.manchester.ac.uk/portal/en/theses/partition-and-turnover-of-glutathione-reductase-in-saccharomyces-cerevisiae-a-proteomic-approach(5f813b0d-4742-4f7a-b4bd-a4e309e9e68c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686711

Loughborough University

10. Da Costa, Caitlyn. Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis.

Degree: PhD, 2016, Loughborough University

URL: https://dspace.lboro.ac.uk/2134/21617 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.693031

► The use of mass spectrometry for the analysis of petrochemical products and crude oils enables the generation of detailed molecular data essential for chemical characterisation… (more)

▼ The use of mass spectrometry for the analysis of petrochemical products and crude oils enables the generation of detailed molecular data essential for chemical characterisation and product development. However, the need for multistage sample preparation techniques can be time consuming and may result in the loss of information. Ambient ionisation in combination with mass spectrometry enables the direct analysis of compounds present on a surface with minimal or no sample preparation. The work presented in this thesis evaluates the application of mass spectrometry (MS) hyphenated with ambient ionisation and ion mobility for the analysis of chemical additives used in lubricant and petrochemical products and also crude oil. A technique called desorption electrospray ionisation (DESI) pioneered the ambient ionisation field. An in-house designed and constructed DESI source has been developed to enable hyphenation of DESI with MS and ion-mobility mass spectrometry (IM-MS) for the interrogation of chemical additives used in lubricant and petrochemical oils directly from multiple surface substrates. The approach has been successfully applied to the analysis of a range of chemical additives as standards and when present in a lubricating oil matrix. Data has also shown that DESI-MS can be used to map additive deposition on a surface. The quantitative capabilities of DESI-MS have been assessed using a lubricant antioxidant additive present in a lubricant oil matrix and deposited on a surface. The DESI-MS method showed good linearity with a limit of detection (LOD) for the antioxidant additive below that used in typical commercial formulations. The use of a suitable internal standard in the DESI-MS analysis has been shown to significantly improve the repeatability of the approach. Hyphenation of DESI with post ionisation separation methods, such as high field asymmetric waveform ion mobility spectrometry (FAIMS), can improve mass spectral response for targeted analytes through selective transmission. The analysis of a series of corrosion inhibitor additives in a base oil matrix has been carried out using electrospray (ESI) and DESI hyphenated with FAIMS-MS. FAIMS selection of target ions improved the sensitivity of ESI and DESI through enhanced analyte transmission and a reduction in the chemical noise resulting from the oil matrix. DESI-FAIMS-MS was shown to improve target analyte response compared to DESI-MS alone using the corrosion inhibitors as model compounds, showing how the combined technique can be used for the rapid analysis of analytes directly from surfaces with no sample preparation or pre concentration. Direct analysis in real time (DART) is an alternative ambient ionisation approach to DESI. The use of DART-MS for the direct analysis of lubricant and oil additives has been evaluated. All selected additives were successfully detected by DART-MS as standards and in an oil matrix. The surface material, DART helium gas temperature and the presence of an oil matrix were all shown to effect the desorption and ionisation…

Subjects/Keywords: 543; Mass spectrometry; Analytical chemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Da Costa, C. (2016). Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis. (Doctoral Dissertation). Loughborough University. Retrieved from https://dspace.lboro.ac.uk/2134/21617 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.693031

Chicago Manual of Style (16^th Edition):

Da Costa, Caitlyn. “Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis.” 2016. Doctoral Dissertation, Loughborough University. Accessed December 09, 2019. https://dspace.lboro.ac.uk/2134/21617 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.693031.

MLA Handbook (7^th Edition):

Da Costa, Caitlyn. “Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis.” 2016. Web. 09 Dec 2019.

Vancouver:

Da Costa C. Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis. [Internet] [Doctoral dissertation]. Loughborough University; 2016. [cited 2019 Dec 09]. Available from: https://dspace.lboro.ac.uk/2134/21617 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.693031.

Council of Science Editors:

Da Costa C. Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis. [Doctoral Dissertation]. Loughborough University; 2016. Available from: https://dspace.lboro.ac.uk/2134/21617 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.693031

University of Manchester

11. Reamtong, Onrapak. The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide.

Degree: PhD, 2010, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/the-identification-and-characterisation-of-the-target-proteins-of-the-antiepileptic-drug-rlacosamide(2e2e4b3b-4101-46e3-886f-ff56c62d2b59).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518815

► (2R)-N-Benzyl-2-acetamido-3-methoxypropionamide (lacosamide) is an anticonvulsant (Choi et al., 1996); under the brand name "Vimpat" this small molecule has recently been approved by the European Medicines… (more)

▼ (2R)-N-Benzyl-2-acetamido-3-methoxypropionamide (lacosamide) is an anticonvulsant (Choi et al., 1996); under the brand name "Vimpat" this small molecule has recently been approved by the European Medicines Agency and the U.S. Food and Drug Administration for the treatment of epilepsy. The purpose of the research reported here is to develop and apply mass spectrometry approaches to the determination of protein targets of this novel therapeutic. The general strategy involves selecting potential target proteins using lacosamide analogues incorporating an 'affinity bait' to enable covalent modification binding to target proteins, and a 'chemical reporter' for the selective recovery of modified proteins. Lacosamide analogues are incubated with biological samples (primarily mouse brain extracts) and the modified proteins are recovered by introduction of a biotin tag (via the chemical reporter group). Streptavidin affinity chromatography is then used to enrich for bound molecules. The enriched proteins are subjected to tryptic digestion and the resultant peptides analysed by reversed phase liquid chromatography coupled with tandem MS, enabling recognition of proteins via database searching. Firstly, mass spectrometric characterisation of the biotinyl (R)-lacosamide analogue bound to model compounds was performed. Adducts with protected lysine, neurotensin and enolase were analysed. The data showed that ESI was more suitable for ionisation of modified peptides and proteins than MALDI. The biotin enrichment strategy was applied to mouse brain lysate to identify putative candidate target proteins. Twenty-eight candidate target proteins were identified. Moreover, the 14-3-3 protein family, CRMP2 and the sodium/potassium-transporting ATPase family showed preference for the biologically active(R)- isomer over the (S)- lacosamide analogue using a fluorescence tag. Three more biotinyl lacosamide analogues containing different affinity baits were used to enrich candidate target proteins of lacosamide. Most of the identified target proteins supported the findings of the analogue A. To indicate the binding sites, a method was developed for enriching peptides modified by the biotinyl (R)-lacosamide analogue, using streptavidin beads and subsequently analysed these biotinylated peptides using CID and ETD fragmentation methods. Neither fragmentation technique was optimal for elucidation of the sequence or site of modification of unknown target peptides. Purified recombinant proteins were therefore adducted with an AB-(R)-lacosamide analogue lacking the biotinprobe. This smaller (R)-lacosamide analogue underwent less fragmentation than the biotin analogue during CID and could be used for sequence and site identification of the modified peptides. In summary, the studies illustrated the power of MS to study drug mechanisms via the discovery of candidate protein targets.

Subjects/Keywords: 615; Mass spectrometry; lacosamide

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Reamtong, O. (2010). The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/the-identification-and-characterisation-of-the-target-proteins-of-the-antiepileptic-drug-rlacosamide(2e2e4b3b-4101-46e3-886f-ff56c62d2b59).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518815

Chicago Manual of Style (16^th Edition):

Reamtong, Onrapak. “The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide.” 2010. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/the-identification-and-characterisation-of-the-target-proteins-of-the-antiepileptic-drug-rlacosamide(2e2e4b3b-4101-46e3-886f-ff56c62d2b59).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518815.

MLA Handbook (7^th Edition):

Reamtong, Onrapak. “The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide.” 2010. Web. 09 Dec 2019.

Vancouver:

Reamtong O. The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide. [Internet] [Doctoral dissertation]. University of Manchester; 2010. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/the-identification-and-characterisation-of-the-target-proteins-of-the-antiepileptic-drug-rlacosamide(2e2e4b3b-4101-46e3-886f-ff56c62d2b59).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518815.

Council of Science Editors:

Reamtong O. The identification and characterisation of the target proteins of the anti-epileptic drug R-lacosamide. [Doctoral Dissertation]. University of Manchester; 2010. Available from: https://www.research.manchester.ac.uk/portal/en/theses/the-identification-and-characterisation-of-the-target-proteins-of-the-antiepileptic-drug-rlacosamide(2e2e4b3b-4101-46e3-886f-ff56c62d2b59).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518815

University of Manchester

12. Lee, Dave. Informatics tools for the analysis and assignment of phosphorylation status in proteomics.

Degree: PhD, 2015, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/informatics-tools-for-the-analysis-and-assignment-of-phosphorylation-status-in-proteomics(48d2cc82-5bb2-4f07-9cdd-670467db4378).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.644464

► Presently, progress in the field of phosphoproteomics has been accelerated by mass spectrometry. This is not a surprise owing to not only the accuracy, precision… (more)

▼ Presently, progress in the field of phosphoproteomics has been accelerated by mass spectrometry. This is not a surprise owing to not only the accuracy, precision and high-throughput capabilities of MS but also due to the support it receives from informaticians whom allow the automated analysis; making the task of going from a complex sample to a statistically satisfactory set of phosphopeptides and corresponding site positions with relative ease. However, the process of identifying and subsequently pinpointing the phosphorylation moiety is not straightforward and remains a challenging task. Furthermore, it has been suggested that not all phosphorylation sites are of equal functional importance, to the extent that some may even lack function altogether. Clearly, such sites will confound the efforts towards functional characterisation. The work in this thesis is aimed at these two issues; accurate site localisation and functional annotation. To address the first issue, I adopt a multi-tool approach for identification and site localisation; utilising the different underlying algorithms of each tool and thereby allowing an orthogonal perspective on the same tandem mass spectra. Doing so enhanced accuracy over any single tool by itself. The power of this multi-tool approach stemmed from its ability to not predict more true positives but rather by removal of false positives. For the second issue, I first investigated the hypothesis that those of functional consequence exhibit stronger phosphorylation-characteristic features such as the degree of conservation and disorder. Indeed, it was found that some features were enriched for the functional group. More surprisingly, there were also some that were enriched for the less-functional; suggesting their incorporation into a prediction algorithm would hinder functional prediction. With this in mind, I train and optimise several machine-learning algorithms, using different combinations of features in an attempt to (separately) improve general phosphorylation and functional prediction.

Subjects/Keywords: 572; Phosphorylation; Mass spectrometry; Functional

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APA (6^th Edition):

Lee, D. (2015). Informatics tools for the analysis and assignment of phosphorylation status in proteomics. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/informatics-tools-for-the-analysis-and-assignment-of-phosphorylation-status-in-proteomics(48d2cc82-5bb2-4f07-9cdd-670467db4378).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.644464

Chicago Manual of Style (16^th Edition):

Lee, Dave. “Informatics tools for the analysis and assignment of phosphorylation status in proteomics.” 2015. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/informatics-tools-for-the-analysis-and-assignment-of-phosphorylation-status-in-proteomics(48d2cc82-5bb2-4f07-9cdd-670467db4378).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.644464.

MLA Handbook (7^th Edition):

Lee, Dave. “Informatics tools for the analysis and assignment of phosphorylation status in proteomics.” 2015. Web. 09 Dec 2019.

Vancouver:

Lee D. Informatics tools for the analysis and assignment of phosphorylation status in proteomics. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/informatics-tools-for-the-analysis-and-assignment-of-phosphorylation-status-in-proteomics(48d2cc82-5bb2-4f07-9cdd-670467db4378).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.644464.

Council of Science Editors:

Lee D. Informatics tools for the analysis and assignment of phosphorylation status in proteomics. [Doctoral Dissertation]. University of Manchester; 2015. Available from: https://www.research.manchester.ac.uk/portal/en/theses/informatics-tools-for-the-analysis-and-assignment-of-phosphorylation-status-in-proteomics(48d2cc82-5bb2-4f07-9cdd-670467db4378).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.644464

University of Manchester

13. Henderson, Fiona Rae. Mass Spectrometry Imaging of Lipid Profiles in Disease.

Degree: 2017, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308361

► It is well established that lipids play an important role in diseases such as non-alcoholic fatty liver disease and cardiovascular diseases. However, in the past… (more)

▼ It is well established that lipids play an important role in diseases such as non-alcoholic fatty liver disease and cardiovascular diseases. However, in the past decade, it has come to light that lipids may be important in other diseases; particularly in cancer and neurological disorders. Here, lipid metabolism has been investigated using pre-clinical cancer models for melanoma, glioma, non-small-cell lung cancer and colorectal cancer. The role of lipids in the recovery post-stroke has also been studied. Mass spectrometry imaging offers an ideal tool to study lipids in tissue ex-vivo. Lipids ionise well in a number of mass spectrometry modalities, and hundreds of lipids can be imaged in one mass spectrometry imaging experiment. Furthermore, mass spectrometry imaging offers excellent spatial resolution. In this work, both MALDI-MS and DESI-MS have been used for mass spectrometry imaging.Tumour lipid heterogeneity has been a particular focus of this this project. Heterogeneity exists within tumours, as well as between tumours in the same patient; and this causes major problems for therapy. Owing to the untargeted nature, and high spatial resolution of mass spectrometry imaging, it is an excellent technique to study lipid heterogeneity. Adjacent sections (or in some cases the same section used for mass spectrometry imaging), were used for immunofluorescence and H&E staining. By comparing mass spectrometry images with staining techniques, biological reasons for lipid heterogeneity can be established. Here, a particular focus has been on hypoxia (low oxygen tensions), which is a key contributor to tumour heterogeneity, and is associated with aggressive cancers. Additionally, hypoxia is a feature of ischaemic stroke, and lipids in ischaemic stroke have also been investigated. PET is a non-invasive imaging technique which is able to image a radiolabelled molecule (tracer) in the body. Here, PET has been used as a complementary in-vivo technique to mass spectrometry imaging. The tracers [11C] acetate and [18F]-FTHA have been used to image fatty acid synthase and fatty acid uptake in tumours; both of which are hypothesised to be key in cancer progression. REIMS is a newly established mass spectrometry technique. It is ideal for analysing lipids in cells, as sample preparation is minimal. Here, approaches for cell pellet analysis have been tested, and used to detect lipids in cancer cell lines. Advisors/Committee Members: MCMAHON, ADAM AW, Williams, Kaye, Mcmahon, Adam.

Subjects/Keywords: Mass spectrometry imaging; Lipids; Cancer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Henderson, F. R. (2017). Mass Spectrometry Imaging of Lipid Profiles in Disease. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308361

Chicago Manual of Style (16^th Edition):

Henderson, Fiona Rae. “Mass Spectrometry Imaging of Lipid Profiles in Disease.” 2017. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308361.

MLA Handbook (7^th Edition):

Henderson, Fiona Rae. “Mass Spectrometry Imaging of Lipid Profiles in Disease.” 2017. Web. 09 Dec 2019.

Vancouver:

Henderson FR. Mass Spectrometry Imaging of Lipid Profiles in Disease. [Internet] [Doctoral dissertation]. University of Manchester; 2017. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308361.

Council of Science Editors:

Henderson FR. Mass Spectrometry Imaging of Lipid Profiles in Disease. [Doctoral Dissertation]. University of Manchester; 2017. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:308361

University of Manchester

14. Bromilow, Sophie. Proteomics in â€˜Free-fromâ€™ Foods.

Degree: 2018, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:314289

► Wheat is the most agronomically important crop with an annual production of approximately 680 million tonnes per year over the five year period of 2008-2012… (more)

▼ Wheat is the most agronomically important crop with an annual production of approximately 680 million tonnes per year over the five year period of 2008-2012 (Shewry and Tatham 2016). Wheat typically contributes about 20% of the total calorie intake in Western Europe and between 50-70% in some countries in North Africa and in West and Central Asia. It is estimated that in order to meet the continuous growing global demand wheat production needs to increase by 50% by 2050. Wheat is most commonly consumed as bread, pasta and noodles however it is also used as a food ingredient in other types of foods such as sauces and condiments. The versatility of wheat is largely determined by the unique physiochemical properties of gluten (Bailey 1941). Gluten is one of the earliest proteins to be studied, and was first described by Beccari in 1728 (Bailey 1941) and is readily isolated from wheat flour as a viscoelastic mass. Gluten is a complex mixture of proteins which are the major seed storage proteins found in the cereal grains wheat, barley, rye and oats. Gluten accounts for 70-80% of the total protein content in wheat grains and is traditionally divided into two groups based on their solubility called gliadins and glutenins (Osborne 1907). In genetically pre-disposed patients gluten is able to elicit a non-IgE mediated T-cell response known as coeliac disease (CD). CD affects approximately 1% of the global population for which there is no cure. As no cure is available patients must adhere to a strict gluten-free diet which is often costly and socially excluding. The Codex Standard states that gluten-free foods must contain less than 20 ppm of gluten from wheat, barley, rye and oats and their crossbreeds (FAO/WHO 1983). The Codex Standard also recommends using immunobased methods (or alternative methods) that are able to achieve appropriate sensitivity and specificity for the detection and quantification of gluten with a 10 ppm limit of detection (FAO/WHO 1983). Consequently the current gold standard method for detection of gluten is enzyme linked immunosorbent assay (ELISA) utilising the R5 antibody, however this method is not without shortcomings. Proteomics by mass spectrometry has the potential to offer an alternative, complementary method to determine gluten proteins in foods but for the methodology to become fully validated and accepted it must also overcome similar challenges to immunoassay methods, such as effective extraction of samples and the identification of peptide targets with the requisite specificity. In this research a global approach is taken to aid the development of gluten detection methods using mass spectrometry. One of the major hurdles that has stunted the development of mass spectrometry methods for the detection and quantification for gluten is the lack of protein sequence databases which are required to undertake the MS data searching. In the first results chapter of the thesis a curated gluten protein sequence database was developed (GluPro), and investigated for its utility as a MS data searching… Advisors/Committee Members: BUCKLEY, MICHAEL M, Mills, Clare, Buckley, Michael.

Subjects/Keywords: proteomics; gluten; mass spectrometry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bromilow, S. (2018). Proteomics in â€˜Free-fromâ€™ Foods. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:314289

Chicago Manual of Style (16^th Edition):

Bromilow, Sophie. “Proteomics in â€˜Free-fromâ€™ Foods.” 2018. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:314289.

MLA Handbook (7^th Edition):

Bromilow, Sophie. “Proteomics in â€˜Free-fromâ€™ Foods.” 2018. Web. 09 Dec 2019.

Vancouver:

Bromilow S. Proteomics in â€˜Free-fromâ€™ Foods. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:314289.

Council of Science Editors:

Bromilow S. Proteomics in â€˜Free-fromâ€™ Foods. [Doctoral Dissertation]. University of Manchester; 2018. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:314289

University of Manchester

15. Dickinson, Eleanor Rose. Characterising Disordered Proteins of the Cancer Genome using Biophysical Techniques.

Degree: 2017, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307062

► Protein function and dysfunction, and their intimate ties to protein structure, has been a core focus of research for several decades. More recently, research into… (more)

▼ Protein function and dysfunction, and their intimate ties to protein structure, has been a core focus of research for several decades. More recently, research into the lack of structure in proteins has reached fever pitch. Intrinsically disordered proteins (IDPs) are proteins (or protein regions) that exist as collapsed or extended, dynamically mobile conformational ensembles, either at secondary or tertiary level, whilst remaining biologically active. The properties of IDPs can impede their study; they are often inherently unstable, are vastly wide-ranging in molecular weight and often difficult to express in large quantities. Mass spectrometry (MS) has evolved into a tool for the study of dynamic systems such as IDPs due to its large dynamic range, high sensitivity, low sample consumption and its lack of bias towards the folded state of a protein. The addition of ion mobility separation to mass spectrometry analysis (IM-MS) provides insight into the conformations adopted by proteins and their complexes, measuring their rotationally averaged collision cross section which can be compared with coordinates from other biophysical techniques such as X-ray crystallography, NMR and to molecular modelling. The work presented in this thesis uses both MS and IM-MS, along with several other biophysical techniques, to interrogate a number of IDPs which are implicated in cancer.Firstly, variable temperature IM-MS is used to probe several proteins of increasing disorder; structured protein cytochrome c, the tumour suppressor protein p53 and the oncoprotein Murine Double Minute 2 (Mdm2), performing IM-MS measurements at a range of temperature from 200 K to 571 K to elucidate the gas-phase unfolding behaviour of each protein. The interaction between p53 and Mdm2 is a current target for cancer drug therapy. Hence MS and IM-MS, alongside circular dichroism and hydrogen-deuterium exchange are next employed to determine the effect of several known small molecule ligands on the conformations adopted by these disordered domains. The significant structuring of both of these disordered proteins upon binding to their respective ligands can be observed using IM-MS, but is not apparent when using other biophysical techniques, highlighting the ability of IM-MS to capture conformational changes occurring in solution on a short timescale. The regulation of disorder in cells is postulated to be mediated by proline residues. I investigate the impact of proline replacement on the populations of conformers presented by p53 using a range of mutants and then go on to study how these mutations impact upon the binding stoichiometry, affinity and conformational preference of p53 for its interaction partner Mdm2. Finally, the disordered melanoma associated antigen 4 MAGE-A4, and its ability to bind to p53 and block its transcriptional activity is probed using MS and IM-MS. Advisors/Committee Members: WALTHO, JONATHAN JP, Barran, Perdita, Waltho, Jonathan.

Subjects/Keywords: IDP; Protein; p53; mass spectrometry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dickinson, E. R. (2017). Characterising Disordered Proteins of the Cancer Genome using Biophysical Techniques. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307062

Chicago Manual of Style (16^th Edition):

Dickinson, Eleanor Rose. “Characterising Disordered Proteins of the Cancer Genome using Biophysical Techniques.” 2017. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307062.

MLA Handbook (7^th Edition):

Dickinson, Eleanor Rose. “Characterising Disordered Proteins of the Cancer Genome using Biophysical Techniques.” 2017. Web. 09 Dec 2019.

Vancouver:

Dickinson ER. Characterising Disordered Proteins of the Cancer Genome using Biophysical Techniques. [Internet] [Doctoral dissertation]. University of Manchester; 2017. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307062.

Council of Science Editors:

Dickinson ER. Characterising Disordered Proteins of the Cancer Genome using Biophysical Techniques. [Doctoral Dissertation]. University of Manchester; 2017. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:307062

University of Manchester

16. Marsden, Nicholas. The development of an aerosol time-of-flight mass spectrometer for the measurement of mineral dust.

Degree: 2017, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:310052

► The development of new analytical techniques is one of the driving forces in the advancement of scientific understanding. The measurement of the properties of aerosol… (more)

▼ The development of new analytical techniques is one of the driving forces in the advancement of scientific understanding. The measurement of the properties of aerosol particles is an active area of research due to the impact aerosol has on atmospheric processes. Single particle size and composition are key properties that govern many atmospheric processes, but the measurement of these properties is challenging due to the large dynamic range of size and composition that exists in the environment. Mineral dust represents a significant fraction of the global aerosol mass loading and has a profound impact on the earth's radiative budget through the direct interaction with solar and terrestrial radiation, and by affecting microphysical properties of clouds. In addition, mineral dust is involved in the geochemical cycling of many compounds that are vital for the health and vitality of ecosystems. The importance of the chemical and crystallographic properties of a material, or mineral phase, has been highlighted recently. Measurements of the elemental composition of single particles is possible with off-line analysis of dust collected on filters , but mineral phase is usually obtained from X-ray diffraction of bulk samples. These techniques are labour intensive and the lack of ambient measurements is a limiting factor in the development of models that attempt to resolve the complexity of atmospheric processes. Time-of-flight mass spectrometry (TOF-MS) is well suited to on-line single particle composition measurements due its sensitivity and high temporal resolution. Single particle mass spectrometry (SPMS) is a class of TOF-MS technique that is able to identify mineral dust particles from their chemical signature in the mass spectrum. Analysis of refractory mineral dust by mass spectrometry requires laser desorption ionisation (LDI) by high energy pulsed lasers, a process that renders the composition measurement non-quantitative due to incomplete ionisation and matrix effects. Consequently, the identification of mineral phase is not possible because the reproducibility of the measurement is lower than the natural variation between common minerals. This thesis reports the development of a commercially available single particle mass spectrometer for the measurement of the physiochemical properties of mineral dust. The optical particle detection system is improved for the more efficient detection of single particles in the size range relevant to the ambient measurement of mineral dust aerosol, and a model is developed that will aid the further development of particle detection in SPMS. A novel method for the on-line differentiation of mineral phase in single particles is presented which exploits differences in ion arrival times at the TOF-MS detector of a silicate molecular ion species, that arise from the influence of mineral phase on the ion formation process during the LDI process. The efficacy of the technique is demonstrated with the differentiation of mineral phase in laboratory generated mineral dust from clay mineral… Advisors/Committee Members: ALLAN, JAMES JD, Coe, Hugh, Allan, James.

Subjects/Keywords: Aerosol; Mass Spectrometry; Mineral Dust

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Marsden, N. (2017). The development of an aerosol time-of-flight mass spectrometer for the measurement of mineral dust. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:310052

Chicago Manual of Style (16^th Edition):

Marsden, Nicholas. “The development of an aerosol time-of-flight mass spectrometer for the measurement of mineral dust.” 2017. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:310052.

MLA Handbook (7^th Edition):

Marsden, Nicholas. “The development of an aerosol time-of-flight mass spectrometer for the measurement of mineral dust.” 2017. Web. 09 Dec 2019.

Vancouver:

Marsden N. The development of an aerosol time-of-flight mass spectrometer for the measurement of mineral dust. [Internet] [Doctoral dissertation]. University of Manchester; 2017. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:310052.

Council of Science Editors:

Marsden N. The development of an aerosol time-of-flight mass spectrometer for the measurement of mineral dust. [Doctoral Dissertation]. University of Manchester; 2017. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:310052

University of Manchester

17. Lee, Dave. Informatics tools for the analysis and assignment of phosphorylation status in proteomics.

Degree: 2015, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259036

►

Presently, progress in the field of phosphoproteomics has been accelerated by mass spectrometry. This is not a surprise owing to not only the accuracy, precision… (more)

▼

Presently, progress in the field of phosphoproteomics has been accelerated by mass spectrometry. This is not a surprise owing to not only the accuracy, precision and high-throughput capabilities of MS but also due to the support it receives from informaticians whom allow the automated analysis; making the task of going from a complex sample to a statistically satisfactory set of phosphopeptides and corresponding site positions with relative ease. However, the process of identifying and subsequently pinpointing the phosphorylation moiety is not straightforward and remains a challenging task. Furthermore, it has been suggested that not all phosphorylation sites are of equal functional importance, to the extent that some may even lack function altogether. Clearly, such sites will confound the efforts towards functional characterisation. The work in this thesis is aimed at these two issues; accurate site localisation and functional annotation. To address the first issue, I adopt a multi-tool approach for identification and site localisation; utilising the different underlying algorithms of each tool and thereby allowing an orthogonal perspective on the same tandem mass spectra. Doing so enhanced accuracy over any single tool by itself. The power of this multi-tool approach stemmed from its ability to not predict more true positives but rather by removal of false positives. For the second issue, I first investigated the hypothesis that those of functional consequence exhibit stronger phosphorylation-characteristic features such as the degree of conservation and disorder. Indeed, it was found that some features were enriched for the functional group. More surprisingly, there were also some that were enriched for the less-functional; suggesting their incorporation into a prediction algorithm would hinder functional prediction. With this in mind, I train and optimise several machine-learning algorithms, using different combinations of features in an attempt to (separately) improve general phosphorylation and functional prediction.

Phosphorylation is a key post-translational modification that is deeply embedded within the biological system. Its role, either directly or indirectly, is regulatory where it is responsible for a vast number of biological processes. As such, the task of pinpointing their precise locations and subsequently attempting to characterise their functional role is an active area of research. Presently, mass spectrometry-based strategies are the major players in the field of phosphoproteomics due to their ability to acquire a global snapshot of the phosphoproteome with relative ease and having an arsenal of software tools to process the data. This latter stage of identifying phosphopeptides and then pinpointing the precise phosphosite is a major challenge in the field. One reason in particular is that different software tools do not always agree with each other; causing confusion regarding the true identity of the site in question. However, even if one is able to perfectly pinpoint the phosphosite, they…

Advisors/Committee Members: WARWICKER, JIM J, Eyers, Claire, Hubbard, Simon, Warwicker, Jim.

Subjects/Keywords: Phosphorylation; Mass spectrometry; Functional

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Lee, D. (2015). Informatics tools for the analysis and assignment of phosphorylation status in proteomics. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259036

Chicago Manual of Style (16^th Edition):

Lee, Dave. “Informatics tools for the analysis and assignment of phosphorylation status in proteomics.” 2015. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259036.

MLA Handbook (7^th Edition):

Lee, Dave. “Informatics tools for the analysis and assignment of phosphorylation status in proteomics.” 2015. Web. 09 Dec 2019.

Vancouver:

Lee D. Informatics tools for the analysis and assignment of phosphorylation status in proteomics. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259036.

Council of Science Editors:

Lee D. Informatics tools for the analysis and assignment of phosphorylation status in proteomics. [Doctoral Dissertation]. University of Manchester; 2015. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259036

University of Manchester

18. Bromilow, Sophie. Proteomics in 'free-from' foods.

Degree: PhD, 2018, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/proteomics-in-afreefroma-foods(5793f2a1-9552-46e1-92b4-2fce7fadaa27).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740423

► Wheat is the most agronomically important crop with an annual production of approximately 680 million tonnes per year over the five year period of 2008-2012… (more)

▼ Wheat is the most agronomically important crop with an annual production of approximately 680 million tonnes per year over the five year period of 2008-2012 (Shewry and Tatham 2016). Wheat typically contributes about 20% of the total calorie intake in Western Europe and between 50-70% in some countries in North Africa and in West and Central Asia. It is estimated that in order to meet the continuous growing global demand wheat production needs to increase by 50% by 2050. Wheat is most commonly consumed as bread, pasta and noodles however it is also used as a food ingredient in other types of foods such as sauces and condiments. The versatility of wheat is largely determined by the unique physiochemical properties of gluten (Bailey 1941). Gluten is one of the earliest proteins to be studied, and was first described by Beccari in 1728 (Bailey 1941) and is readily isolated from wheat flour as a viscoelastic mass. Gluten is a complex mixture of proteins which are the major seed storage proteins found in the cereal grains wheat, barley, rye and oats. Gluten accounts for 70-80% of the total protein content in wheat grains and is traditionally divided into two groups based on their solubility called gliadins and glutenins (Osborne 1907). In genetically pre-disposed patients gluten is able to elicit a non-IgE mediated T-cell response known as coeliac disease (CD). CD affects approximately 1% of the global population for which there is no cure. As no cure is available patients must adhere to a strict gluten-free diet which is often costly and socially excluding. The Codex Standard states that gluten-free foods must contain less than 20 ppm of gluten from wheat, barley, rye and oats and their crossbreeds (FAO/WHO 1983). The Codex Standard also recommends using immunobased methods (or alternative methods) that are able to achieve appropriate sensitivity and specificity for the detection and quantification of gluten with a 10 ppm limit of detection (FAO/WHO 1983). Consequently the current gold standard method for detection of gluten is enzyme linked immunosorbent assay (ELISA) utilising the R5 antibody, however this method is not without shortcomings. Proteomics by mass spectrometry has the potential to offer an alternative, complementary method to determine gluten proteins in foods but for the methodology to become fully validated and accepted it must also overcome similar challenges to immunoassay methods, such as effective extraction of samples and the identification of peptide targets with the requisite specificity. In this research a global approach is taken to aid the development of gluten detection methods using mass spectrometry. One of the major hurdles that has stunted the development of mass spectrometry methods for the detection and quantification for gluten is the lack of protein sequence databases which are required to undertake the MS data searching. In the first results chapter of the thesis a curated gluten protein sequence database was developed (GluPro), and investigated for its utility as a MS data searching…

Subjects/Keywords: mass spectrometry; proteomics; gluten

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bromilow, S. (2018). Proteomics in 'free-from' foods. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/proteomics-in-afreefroma-foods(5793f2a1-9552-46e1-92b4-2fce7fadaa27).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740423

Chicago Manual of Style (16^th Edition):

Bromilow, Sophie. “Proteomics in 'free-from' foods.” 2018. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/proteomics-in-afreefroma-foods(5793f2a1-9552-46e1-92b4-2fce7fadaa27).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740423.

MLA Handbook (7^th Edition):

Bromilow, Sophie. “Proteomics in 'free-from' foods.” 2018. Web. 09 Dec 2019.

Vancouver:

Bromilow S. Proteomics in 'free-from' foods. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/proteomics-in-afreefroma-foods(5793f2a1-9552-46e1-92b4-2fce7fadaa27).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740423.

Council of Science Editors:

Bromilow S. Proteomics in 'free-from' foods. [Doctoral Dissertation]. University of Manchester; 2018. Available from: https://www.research.manchester.ac.uk/portal/en/theses/proteomics-in-afreefroma-foods(5793f2a1-9552-46e1-92b4-2fce7fadaa27).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740423

University of Edinburgh

19. Thurlow, Sophie Erica. Investigating redox posttranslational modifications in proteins using mass spectrometry.

Degree: PhD, 2015, University of Edinburgh

URL: http://hdl.handle.net/1842/18020

► Redox potential, a measure of how oxidising or reducing an environment is, is tightly regulated by cells to minimise detrimental chemical oxidation and reduction reactions.… (more)

▼ Redox potential, a measure of how oxidising or reducing an environment is, is tightly regulated by cells to minimise detrimental chemical oxidation and reduction reactions. In proteins, it is the sulfur containing cysteine residues that can be post-translationally modified through specific redox reactions, for example, the formation of disulfide bonds between cysteine residues can be crucial to protein structure. It has recently been hypothesised that signalling pathways utilising redox regulated proteins may be arranged into electrochemical series. The characterisation of the redox properties of specific cysteine residues in proteins has proven difficult using traditional redox characterisation methods such as cyclic voltammetry. A number of biochemical methods have been developed for studying the effect of the redox environment on proteins, many making use of mass spectrometry and allowing for localisation of the site of the modification to specific cysteine residues. However, fewer methods have been reported that facilitate accurate quantification for the determination of the mid-point potential of these redox regulated cysteine residues. Here, a differential labelling protocol using high resolution mass spectrometry techniques for the study of redox chemistry of cysteine residues in proteins will be reported. The protocol exploits the novel chemistry of thiol groups for specific alkylation and allows for both qualitative and quantitative experiments. Thioredoxin-1 from E. coli and human systems was used as a model protein and a novel disulfide bond was characterised. The reducing potential of the active site cysteine residues of human thioredoxin were found to be very similar to those of the E. coli proteoform, -276 ± 1 and -281.4 ± 0.3 mV respectively. The remaining three cysteine residues of human thioredoxin were found to be regulated at more oxidising potentials. The protocol developed was applied to a protein from the cell death pathway of apoptosis; human caspase-3 is an executioner protease from the caspase cascade. Caspase-3 was found to contain three redox sensitive cysteine residues. The catalytically active cysteine residue was redox regulated via two mechanisms, glutathionylation and disulfide bond formation. One of these mechanisms gives the active site cysteine residue a calculated reducing potential of -165 ± 6 mV supporting the correlation between caspase-3 activity and its observed role in the apoptotic pathway but not in necrotic cell death.

Subjects/Keywords: 543; mass spectrometry; proteins; redox

Record Details Similar Records Cite « Share

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Thurlow, S. E. (2015). Investigating redox posttranslational modifications in proteins using mass spectrometry. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/18020

Chicago Manual of Style (16^th Edition):

Thurlow, Sophie Erica. “Investigating redox posttranslational modifications in proteins using mass spectrometry.” 2015. Doctoral Dissertation, University of Edinburgh. Accessed December 09, 2019. http://hdl.handle.net/1842/18020.

MLA Handbook (7^th Edition):

Thurlow, Sophie Erica. “Investigating redox posttranslational modifications in proteins using mass spectrometry.” 2015. Web. 09 Dec 2019.

Vancouver:

Thurlow SE. Investigating redox posttranslational modifications in proteins using mass spectrometry. [Internet] [Doctoral dissertation]. University of Edinburgh; 2015. [cited 2019 Dec 09]. Available from: http://hdl.handle.net/1842/18020.

Council of Science Editors:

Thurlow SE. Investigating redox posttranslational modifications in proteins using mass spectrometry. [Doctoral Dissertation]. University of Edinburgh; 2015. Available from: http://hdl.handle.net/1842/18020

University of Manchester

20. Theisen, Alina. Combining UVPD and IM-MS for structural analysis of biomolecules.

Degree: 2019, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318061

► Proteins are crucial for virtually all cellular processes and life; studying the way they fold into three-dimensional structures, or the lack of defined structure, and… (more)

▼ Proteins are crucial for virtually all cellular processes and life; studying the way they fold into three-dimensional structures, or the lack of defined structure, and their dynamics is therefore imperative. Ion mobility mass spectrometry is ideally suited for obtaining global structural information, but requires coupling with other methods to afford local structural details. We have modified a Synapt G2-S to enable ultraviolet photodissociation, a fast and structurally-sensitive fragmentation method, of mass-selected ions either prior to or post ion mobility separation. Using 266 nm photons, we first demonstrate the capabilities of the instrument by sequencing peptides LHRH, GHRP-6 and the mini protein TrpCage. Mobility-selection allows separate UVPD spectra to be obtained for the m/z coincident Gramicidin A monomer and dimer, revealing differences in fragmentation patterns. Synchronising a single laser pulse to the start of the mobility-cycle allows discrimination between primary and secondary fragments. We also observe distinct spectra for two conformational families of 5+ melittin, indicating that UVPD at 266 nm may be conformer-dependent. We then applied our methodology to the proteins ubiquitin, cytochrome c and myoglobin using 213 nm photons. UVPD was carried out pre-ion mobility at different source conditions which altered the conformations prior to UVPD. Initial unfolding resulted in increased fragmentation yield as well as an increase in cleavage sites, which when mapped onto crystal structures revealed the sites in which initial unfolding occurred. We hypothesised that the differences in compact to extended UVPD spectra may be due to non-covalently linked fragments originating from folded precursors, and tested this by collisionally activating photoproducts post ion mobility. This revealed an increase in both yield and cleavage sites when applied to compact conformations indicating that non-covalently held fragments are indeed prevalent in UVPD of structured precursor conformations. In harsh source conditions, only cytochrome c exhibited an increase in a-type fragments, indicating that in-source activation resulted in loss of non-covalent bonding for ubiquitin and myoglobin. However, UVPD-IM-CID of compact conformations could not fully replicate the spectra obtained by UVPD of extended conformations even when secondary UVPD was accounted for; therefore it is apparent that inherent differences in the UVPD process exist between conformations. We further modified the source region of the instrument to allow LED irradiation within the sample capillary. For the photoreceptor UVR8, UV-IM-MS comparison of full-length and a truncated version revealed the presence of two distinct conformational families in the wild-type, a compact and a more extended one, due to the presence of disordered C- and N-terminal tails. Our setup allowed us to follow the receptor dynamics upon UV irradiation and postulate a role of the disordered tails in the photo-activation process. Advisors/Committee Members: LOCKYER, NICHOLAS NP, Barran, Perdita, Lockyer, Nicholas.

Subjects/Keywords: Ion mobility; UVPD; Mass Spectrometry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Theisen, A. (2019). Combining UVPD and IM-MS for structural analysis of biomolecules. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318061

Chicago Manual of Style (16^th Edition):

Theisen, Alina. “Combining UVPD and IM-MS for structural analysis of biomolecules.” 2019. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318061.

MLA Handbook (7^th Edition):

Theisen, Alina. “Combining UVPD and IM-MS for structural analysis of biomolecules.” 2019. Web. 09 Dec 2019.

Vancouver:

Theisen A. Combining UVPD and IM-MS for structural analysis of biomolecules. [Internet] [Doctoral dissertation]. University of Manchester; 2019. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318061.

Council of Science Editors:

Theisen A. Combining UVPD and IM-MS for structural analysis of biomolecules. [Doctoral Dissertation]. University of Manchester; 2019. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318061

Loughborough University

21. Da Costa, Caitlyn. Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis.

Degree: PhD, 2016, Loughborough University

URL: http://hdl.handle.net/2134/21617

► The use of mass spectrometry for the analysis of petrochemical products and crude oils enables the generation of detailed molecular data essential for chemical characterisation… (more)

▼ The use of mass spectrometry for the analysis of petrochemical products and crude oils enables the generation of detailed molecular data essential for chemical characterisation and product development. However, the need for multistage sample preparation techniques can be time consuming and may result in the loss of information. Ambient ionisation in combination with mass spectrometry enables the direct analysis of compounds present on a surface with minimal or no sample preparation. The work presented in this thesis evaluates the application of mass spectrometry (MS) hyphenated with ambient ionisation and ion mobility for the analysis of chemical additives used in lubricant and petrochemical products and also crude oil. A technique called desorption electrospray ionisation (DESI) pioneered the ambient ionisation field. An in-house designed and constructed DESI source has been developed to enable hyphenation of DESI with MS and ion-mobility mass spectrometry (IM-MS) for the interrogation of chemical additives used in lubricant and petrochemical oils directly from multiple surface substrates. The approach has been successfully applied to the analysis of a range of chemical additives as standards and when present in a lubricating oil matrix. Data has also shown that DESI-MS can be used to map additive deposition on a surface. The quantitative capabilities of DESI-MS have been assessed using a lubricant antioxidant additive present in a lubricant oil matrix and deposited on a surface. The DESI-MS method showed good linearity with a limit of detection (LOD) for the antioxidant additive below that used in typical commercial formulations. The use of a suitable internal standard in the DESI-MS analysis has been shown to significantly improve the repeatability of the approach. Hyphenation of DESI with post ionisation separation methods, such as high field asymmetric waveform ion mobility spectrometry (FAIMS), can improve mass spectral response for targeted analytes through selective transmission. The analysis of a series of corrosion inhibitor additives in a base oil matrix has been carried out using electrospray (ESI) and DESI hyphenated with FAIMS-MS. FAIMS selection of target ions improved the sensitivity of ESI and DESI through enhanced analyte transmission and a reduction in the chemical noise resulting from the oil matrix. DESI-FAIMS-MS was shown to improve target analyte response compared to DESI-MS alone using the corrosion inhibitors as model compounds, showing how the combined technique can be used for the rapid analysis of analytes directly from surfaces with no sample preparation or pre concentration. Direct analysis in real time (DART) is an alternative ambient ionisation approach to DESI. The use of DART-MS for the direct analysis of lubricant and oil additives has been evaluated. All selected additives were successfully detected by DART-MS as standards and in an oil matrix. The surface material, DART helium gas temperature and the presence of an oil matrix were all shown to effect the desorption and ionisation…

Subjects/Keywords: 543; Mass spectrometry; Analytical chemistry

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APA (6^th Edition):

Da Costa, C. (2016). Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis. (Doctoral Dissertation). Loughborough University. Retrieved from http://hdl.handle.net/2134/21617

Chicago Manual of Style (16^th Edition):

Da Costa, Caitlyn. “Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis.” 2016. Doctoral Dissertation, Loughborough University. Accessed December 09, 2019. http://hdl.handle.net/2134/21617.

MLA Handbook (7^th Edition):

Da Costa, Caitlyn. “Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis.” 2016. Web. 09 Dec 2019.

Vancouver:

Da Costa C. Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis. [Internet] [Doctoral dissertation]. Loughborough University; 2016. [cited 2019 Dec 09]. Available from: http://hdl.handle.net/2134/21617.

Council of Science Editors:

Da Costa C. Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis. [Doctoral Dissertation]. Loughborough University; 2016. Available from: http://hdl.handle.net/2134/21617

University of Manchester

22. Theisen, Alina. Combining UVPD and IM-MS for structural analysis of biomolecules.

Degree: PhD, 2018, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/combining-uvpd-and-imms-for-structural-analysis-of-biomolecules(d2fafe29-b834-436b-8d48-4feea6305aaf).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771370

► Proteins are crucial for virtually all cellular processes and life; studying the way they fold into three-dimensional structures, or the lack of defined structure, and… (more)

▼ Proteins are crucial for virtually all cellular processes and life; studying the way they fold into three-dimensional structures, or the lack of defined structure, and their dynamics is therefore imperative. Ion mobility mass spectrometry is ideally suited for obtaining global structural information, but requires coupling with other methods to afford local structural details. We have modified a Synapt G2-S to enable ultraviolet photodissociation, a fast and structurally-sensitive fragmentation method, of mass-selected ions either prior to or post ion mobility separation. Using 266 nm photons, we first demonstrate the capabilities of the instrument by sequencing peptides LHRH, GHRP-6 and the mini protein TrpCage. Mobility-selection allows separate UVPD spectra to be obtained for the m/z coincident Gramicidin A monomer and dimer, revealing differences in fragmentation patterns. Synchronising a single laser pulse to the start of the mobility-cycle allows discrimination between primary and secondary fragments. We also observe distinct spectra for two conformational families of 5+ melittin, indicating that UVPD at 266 nm may be conformer-dependent. We then applied our methodology to the proteins ubiquitin, cytochrome c and myoglobin using 213 nm photons. UVPD was carried out pre-ion mobility at different source conditions which altered the conformations prior to UVPD. Initial unfolding resulted in increased fragmentation yield as well as an increase in cleavage sites, which when mapped onto crystal structures revealed the sites in which initial unfolding occurred. We hypothesised that the differences in compact to extended UVPD spectra may be due to non-covalently linked fragments originating from folded precursors, and tested this by collisionally activating photoproducts post ion mobility. This revealed an increase in both yield and cleavage sites when applied to compact conformations indicating that non-covalently held fragments are indeed prevalent in UVPD of structured precursor conformations. In harsh source conditions, only cytochrome c exhibited an increase in a-type fragments, indicating that in-source activation resulted in loss of non-covalent bonding for ubiquitin and myoglobin. However, UVPD-IM-CID of compact conformations could not fully replicate the spectra obtained by UVPD of extended conformations even when secondary UVPD was accounted for; therefore it is apparent that inherent differences in the UVPD process exist between conformations. We further modified the source region of the instrument to allow LED irradiation within the sample capillary. For the photoreceptor UVR8, UV-IM-MS comparison of full-length and a truncated version revealed the presence of two distinct conformational families in the wild-type, a compact and a more extended one, due to the presence of disordered C- and N-terminal tails. Our setup allowed us to follow the receptor dynamics upon UV irradiation and postulate a role of the disordered tails in the photo-activation process.

Subjects/Keywords: Ion mobility; UVPD; Mass Spectrometry

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APA (6^th Edition):

Theisen, A. (2018). Combining UVPD and IM-MS for structural analysis of biomolecules. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/combining-uvpd-and-imms-for-structural-analysis-of-biomolecules(d2fafe29-b834-436b-8d48-4feea6305aaf).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771370

Chicago Manual of Style (16^th Edition):

Theisen, Alina. “Combining UVPD and IM-MS for structural analysis of biomolecules.” 2018. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/combining-uvpd-and-imms-for-structural-analysis-of-biomolecules(d2fafe29-b834-436b-8d48-4feea6305aaf).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771370.

MLA Handbook (7^th Edition):

Theisen, Alina. “Combining UVPD and IM-MS for structural analysis of biomolecules.” 2018. Web. 09 Dec 2019.

Vancouver:

Theisen A. Combining UVPD and IM-MS for structural analysis of biomolecules. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/combining-uvpd-and-imms-for-structural-analysis-of-biomolecules(d2fafe29-b834-436b-8d48-4feea6305aaf).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771370.

Council of Science Editors:

Theisen A. Combining UVPD and IM-MS for structural analysis of biomolecules. [Doctoral Dissertation]. University of Manchester; 2018. Available from: https://www.research.manchester.ac.uk/portal/en/theses/combining-uvpd-and-imms-for-structural-analysis-of-biomolecules(d2fafe29-b834-436b-8d48-4feea6305aaf).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771370

University of Manchester

23. Longobardo, Alessia. Mass spectrometric studies of molecules using intense femtosecond laser ionisation.

Degree: PhD, 2012, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometric-studies-of-molecules-using-intense-femtosecond-laser-ionisation(21d80e3c-65fa-449d-9b13-77c0c7695956).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.566547

► Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a sensitive technique used to analyse the molecular composition of solid samples using keV ion beam sputtering. However… (more)

▼ Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a sensitive technique used to analyse the molecular composition of solid samples using keV ion beam sputtering. However only a small fraction (typically < 10⁻³) of the desorbed material issecondary ions - the majority species (neutrals) cannot be extracted and detected by the mass spectrometer. To increase the sensitivity and efficiency of the SIMS technique, post-ionisation above the surface can be used. Lasers have been widely employed for molecular mass spectrometry due to the available high intensity, short pulse width, high spectral purity and spatial coherence that allow them to be highly focused. For molecular samples the challenge is to achieve efficient post-ionisation without inducing extensive fragmentation, which limits the diagnostic value of the resulting mass spectrum. An investigation was performed into the ionisation and dissociation characteristics of a series of organic molecules under the action of intense laser fields. This study is directed towards the analysis of biomolecules using laser post-ionisation. Here is reported progress towards the calibration of the experimental set-up and mass spectral data from representative biomolecules in the gas phase. In this work a Ti:Sapphire laser was used with fundamental wavelength of 800 nm and non-linear optical methods (OPAs) are used to extend the wavelength into the mid-IR region. System calibration is achieved using the ionisation of xenon atoms and comparing the results to established atomic tunnelling theory. This was followed by the analysis of representative organic and biological molecules to study ionisation-dissociation characteristics. The molecules chosen were toluene, acetone, nitroaniline and histamine. A clear transition in behavior is observed favoring molecular ion production. This behavior is discussed in the context of the underlying mechanisms, and the implications for molecular post-ionisation analysis using focused ion beams.

Subjects/Keywords: 543; mass spectrometry; laser post ionisation mass spectrometry

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APA (6^th Edition):

Longobardo, A. (2012). Mass spectrometric studies of molecules using intense femtosecond laser ionisation. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometric-studies-of-molecules-using-intense-femtosecond-laser-ionisation(21d80e3c-65fa-449d-9b13-77c0c7695956).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.566547

Chicago Manual of Style (16^th Edition):

Longobardo, Alessia. “Mass spectrometric studies of molecules using intense femtosecond laser ionisation.” 2012. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometric-studies-of-molecules-using-intense-femtosecond-laser-ionisation(21d80e3c-65fa-449d-9b13-77c0c7695956).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.566547.

MLA Handbook (7^th Edition):

Longobardo, Alessia. “Mass spectrometric studies of molecules using intense femtosecond laser ionisation.” 2012. Web. 09 Dec 2019.

Vancouver:

Longobardo A. Mass spectrometric studies of molecules using intense femtosecond laser ionisation. [Internet] [Doctoral dissertation]. University of Manchester; 2012. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometric-studies-of-molecules-using-intense-femtosecond-laser-ionisation(21d80e3c-65fa-449d-9b13-77c0c7695956).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.566547.

Council of Science Editors:

Longobardo A. Mass spectrometric studies of molecules using intense femtosecond laser ionisation. [Doctoral Dissertation]. University of Manchester; 2012. Available from: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometric-studies-of-molecules-using-intense-femtosecond-laser-ionisation(21d80e3c-65fa-449d-9b13-77c0c7695956).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.566547

24. Harvey, Sophie Rebecca. Biophysical studies into the structure and interactions of proteins and peptides.

Degree: PhD, 2014, University of Edinburgh

URL: http://hdl.handle.net/1842/9654

► Investigating the structure of proteins and their interactions with other biomolecules or drug molecules, coupled with the consideration of conformational change upon binding, is essential… (more)

▼ Investigating the structure of proteins and their interactions with other biomolecules or drug molecules, coupled with the consideration of conformational change upon binding, is essential to better understand their functions. Mass spectrometry (MS) is emerging as a powerful tool to study protein and peptide structure and interactions due to the high dynamic range, low sample consumption and high sensitivity of this technique, providing insight into the stoichiometry, intensity and stability of interactions. The hybrid technique of ion mobility-mass spectrometry (IM-MS) can provide insight into the conformations adopted by protein and peptide monomers and multimers, in addition to complexes resulting from interactions, which when coupled with molecular modelling can suggest candidate conformations for these in vacuo species and by inference their conformations in solution prior to ionisation and desolvation. The work presented in this thesis considers a number of different peptide and protein systems, highlighting how the combination of MS and IM-MS based techniques, in conjunction with other biophysical techniques such as circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM) and isothermal titration calorimetry (ITC) can provide insight into these dynamic systems. First a case study into the ability of MS and IM-MS to study disorder-to-order transitions is presented. The transcription factor c-MYC can only perform its function upon binding with its binding partner MAX; deregulation of c-MYC is, however, implicated in a number of human cancers. c-MYC and MAX comprise intrinsically disordered regions which form a leucine zipper upon binding. The work presented here focuses on the leucine zipper regions of both c-MYC and MAX, their individual conformations and changes upon binding. Inhibiting the c-MYC:MAX interaction is a current target for drug therapy and hence the inhibition of this interaction with a previously identified small drug-like molecule was also examined using these techniques, to determine if such an approach may be appropriate for investigation of future therapeutics. Next the ability of MS-based techniques to preserve, transmit and distinguish between multiple conformations of a metamorphic protein was examined. The chemokine lymphotactin has been shown to exist in two distinct conformations in equilibrium in a ligand-free state. The existence of such metamorphic proteins has called into question whether traditional structural elucidation tools have been inadvertently biased towards consideration of single conformations. Here, the potential of gas-phase techniques in the study of conformationally dynamic systems is examined through the study of wild type lymphotactin and a number of constructs designed either as a minimum model of fold or to mimic one of the distinct folds. Interactions between chemokines and glycosaminoglycans (GAGs) are thought to be essential for the in vivo activity of these proteins. The interactions between the distinctive chemokine lymphotactin and a…

Subjects/Keywords: 572; mass spectrometry; ion mobility-mass spectrometry; proteins

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APA (6^th Edition):

Harvey, S. R. (2014). Biophysical studies into the structure and interactions of proteins and peptides. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/9654

Chicago Manual of Style (16^th Edition):

Harvey, Sophie Rebecca. “Biophysical studies into the structure and interactions of proteins and peptides.” 2014. Doctoral Dissertation, University of Edinburgh. Accessed December 09, 2019. http://hdl.handle.net/1842/9654.

MLA Handbook (7^th Edition):

Harvey, Sophie Rebecca. “Biophysical studies into the structure and interactions of proteins and peptides.” 2014. Web. 09 Dec 2019.

Vancouver:

Harvey SR. Biophysical studies into the structure and interactions of proteins and peptides. [Internet] [Doctoral dissertation]. University of Edinburgh; 2014. [cited 2019 Dec 09]. Available from: http://hdl.handle.net/1842/9654.

Council of Science Editors:

Harvey SR. Biophysical studies into the structure and interactions of proteins and peptides. [Doctoral Dissertation]. University of Edinburgh; 2014. Available from: http://hdl.handle.net/1842/9654

University of Oxford

25. Demetriades, Marina. Dynamic combinatorial mass spectrometry for 2-oxoglutarate oxygenase inhibition.

Degree: PhD, 2013, University of Oxford

URL: http://ora.ox.ac.uk/objects/uuid:8c3a3a33-bc1a-407e-8b86-70c5eca58f38 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639947

► In the last decade, dynamic combinatorial mass spectrometry (DCMS) with protein targets has emerged as a promising method for the identification of enzyme-inhibitors. 2-Oxoglutarate (2OG)… (more)

▼ In the last decade, dynamic combinatorial mass spectrometry (DCMS) with protein targets has emerged as a promising method for the identification of enzyme-inhibitors. 2-Oxoglutarate (2OG) oxygenases are involved in important biological processes related to many diseases; several human 2OG oxygenases are targeted for pharmaceutical intervention. This thesis describes inhibition studies on three 2OG oxygenases using DCMS and structure activity relation (SAR) studies. Disulphide based DCMS was used for the identification of N-oxalyl based lead inhibitors for the 2OG oxygenase AlkB from Escherichia coli. Crystallographic analyses of AlkB with a lead inhibitor assisted in the design of a second generation of inhibitors using N-oxalyl, pyridyl and quinolinyl scaffolds. Crystallographic and kinetic data of three potent and selective AlkB inhibitors validates the DCMS approach for the development of 2OG oxygenase inhibitors. The hypoxia inducible factor hydroxylase, prolyl hydroxylase domain 2 (PHD2), was then used as the model enzyme for the development of a novel DCMS approach employing the reversible reaction of boronic acids with diols to form boronate esters. The ‘boronate’ DCMS method was used to identify pyridyl- substituted lead compounds. Further modification of the pyridine scaffold, based on structural analyses, led to the development of highly potent and selective PHD2 inhibitors. To identify inhibitors for the fat mass and obesity associated protein (FTO), another 2OG oxygenase, an inhibition assay was developed. The inhibition assay was used in conjunction with a differential scanning fluorimetry (DSF) binding assay to identify isoquinolinyl and pyridyl inhibitor scaffolds, related to those used in the DCMS studies. FTO complexed structures of these compounds, and with a natural product anthraquinone, enabled the design and synthesis of new inhibitors that are both co-substrate and substrate competitors of FTO. One such compound proved to be a potent FTO inhibitor with improved selectivity over other 2OG oxygenases. Overall, the work validates the use of DCMS methods for the development of potent and selective inhibitors for 2OG oxygenases, and by implication of other enzyme families.

Subjects/Keywords: 572.8; Organic chemistry; Mass spectrometry; Chemical biology; dynamic combinatorial mass spectrometry; native mass spectrometry; inhibitor design; 2og oxygenases

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APA (6^th Edition):

Demetriades, M. (2013). Dynamic combinatorial mass spectrometry for 2-oxoglutarate oxygenase inhibition. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:8c3a3a33-bc1a-407e-8b86-70c5eca58f38 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639947

Chicago Manual of Style (16^th Edition):

Demetriades, Marina. “Dynamic combinatorial mass spectrometry for 2-oxoglutarate oxygenase inhibition.” 2013. Doctoral Dissertation, University of Oxford. Accessed December 09, 2019. http://ora.ox.ac.uk/objects/uuid:8c3a3a33-bc1a-407e-8b86-70c5eca58f38 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639947.

MLA Handbook (7^th Edition):

Demetriades, Marina. “Dynamic combinatorial mass spectrometry for 2-oxoglutarate oxygenase inhibition.” 2013. Web. 09 Dec 2019.

Vancouver:

Demetriades M. Dynamic combinatorial mass spectrometry for 2-oxoglutarate oxygenase inhibition. [Internet] [Doctoral dissertation]. University of Oxford; 2013. [cited 2019 Dec 09]. Available from: http://ora.ox.ac.uk/objects/uuid:8c3a3a33-bc1a-407e-8b86-70c5eca58f38 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639947.

Council of Science Editors:

Demetriades M. Dynamic combinatorial mass spectrometry for 2-oxoglutarate oxygenase inhibition. [Doctoral Dissertation]. University of Oxford; 2013. Available from: http://ora.ox.ac.uk/objects/uuid:8c3a3a33-bc1a-407e-8b86-70c5eca58f38 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639947

Loughborough University

26. Arthur, Kayleigh L. The development and application of miniaturised FAIMS combined with mass spectrometry in bioanalysis.

Degree: PhD, 2017, Loughborough University

URL: https://dspace.lboro.ac.uk/2134/27724 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.734160

► In this thesis, a miniaturised field asymmetric waveform ion mobility spectrometry (FAIMS) device is combined with mass spectrometry (MS), and liquid chromatography, for the development… (more)

▼ In this thesis, a miniaturised field asymmetric waveform ion mobility spectrometry (FAIMS) device is combined with mass spectrometry (MS), and liquid chromatography, for the development and application of bioanalytical methodologies. FAIMS is a highly orthogonal to MS and LC and has the potential to enhance both targeted and non-targeted bioanalytical applications. Chapter two demonstrates the capability of the FAIMS combined with mass spectrometry to reduce the complexity of the mass spectrum by separating species of different charge states and overlapping mass-to-charge ratios that are challenging to separate by MS. FAIMS selected transmission shows improvement in signal-to-noise ratios for low intensity species and enables visualisation of species undetectable without FAIMS. Chapter three describes the development of an LC-FAIMS-MS method for the rapid analysis of saliva for the identification of potential biomarkers as a result of oxidative stress. The combination of FAIMS showed a reduction in saliva matrix interferences resulting in improved discrimination and peak integration of two salivary oxypurine compounds in a rapid LC-FAIMS-MS method. Chapter four investigates the FAIMS separation of seven steroid metabolites with a range of cationic adducts, in order to develop a rapid screening LC-FAIMS-MS method for the determination of isobaric steroid metabolites in urine. LC-FAIMS-MS analysis of the steroid metabolites shows improved discrimination of co-eluting and isobaric steroid metabolites with improvements in signal-to-noise ratio with reductions in chemical noise, demonstrating the potential of combining FAIMS with LC-MS. Chapter five demonstrates the potential of FAIMS to increase peak capacity in non-targeted omics applications, by combining rapid compensation field scanning of the FAIMS with ultra-high performance LC-MS. The rapid scanning of the FAIMS allows acquisition of full scan FAIMS and MS nested data sets within the timescale of a UHPLC chromatographic peak, and is applied to the non-targeted profiling of human urine. Improvements in the number of features detected using LC-FAIMS-MS were as a result of reductions in chemical noise and separation of co-eluting isobaric species across the whole analytical space, demonstrating the potential of combining FAIMS with LC and MS.

Subjects/Keywords: FAIMS; Mass spectrometry; Ion mobility; Liquid chromatography

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APA (6^th Edition):

Arthur, K. L. (2017). The development and application of miniaturised FAIMS combined with mass spectrometry in bioanalysis. (Doctoral Dissertation). Loughborough University. Retrieved from https://dspace.lboro.ac.uk/2134/27724 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.734160

Chicago Manual of Style (16^th Edition):

Arthur, Kayleigh L. “The development and application of miniaturised FAIMS combined with mass spectrometry in bioanalysis.” 2017. Doctoral Dissertation, Loughborough University. Accessed December 09, 2019. https://dspace.lboro.ac.uk/2134/27724 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.734160.

MLA Handbook (7^th Edition):

Arthur, Kayleigh L. “The development and application of miniaturised FAIMS combined with mass spectrometry in bioanalysis.” 2017. Web. 09 Dec 2019.

Vancouver:

Arthur KL. The development and application of miniaturised FAIMS combined with mass spectrometry in bioanalysis. [Internet] [Doctoral dissertation]. Loughborough University; 2017. [cited 2019 Dec 09]. Available from: https://dspace.lboro.ac.uk/2134/27724 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.734160.

Council of Science Editors:

Arthur KL. The development and application of miniaturised FAIMS combined with mass spectrometry in bioanalysis. [Doctoral Dissertation]. Loughborough University; 2017. Available from: https://dspace.lboro.ac.uk/2134/27724 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.734160

University of Manchester

27. Armitage, Emily Grace. Systems biology of HIF metabolism in cancer.

Degree: PhD, 2012, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/systems-biology-of-hif-metabolism-in-cancer(e237aa18-81a9-4c86-81b1-804555d3585c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559340

► Cancer is one of the most devastating human diseases that cause a vast number of mortalities worldwide each year. Cancer research is one of the… (more)

▼ Cancer is one of the most devastating human diseases that cause a vast number of mortalities worldwide each year. Cancer research is one of the largest fields in the life sciences and despite many astounding breakthroughs and contributions over the past few decades, there is still a considerable amount to unveil on the function of cancer that would improve diagnostics, prognostics and therapy. Since cancer is known to involve a wide range of processes, applying methods to study it from a systems perspective could reveal new properties of cancer. Systems biology is becoming an increasingly popular tool in the life sciences. The approach has been applied to many biological and biomedical analyses drawing upon recent advancements in technology that make high throughput analyses of samples and computational modelling possible. In this thesis, the effect of hypoxia inducible factor-1 (HIF-1) on cancer metabolism, the entity considered most closely related to phenotype has been investigated. This transcription factor is known to regulate a multitude of genes and proteins to promote survival in a low oxygen environment that is prevalent in solid tumours. However its effect on the metabolome is less well characterised. By revealing the effect of HIF-1 on the metabolome as a system it is hoped that phenotypic signatures, key metabolic pathways indicative of cancer function and potential targets for future cancer therapy, can be revealed.The system has been studied using two cell models: mouse hepatocellular carcinoma and human colon carcinoma, whereby metabolism has been profiled using a range of analytical platforms. In each model, wild type cells have been compared to cells deficient in HIF-1 to reveal its effect on cellular metabolism. Gas chromatography mass spectrometry (GC MS) and ultra high performance liquid chromatography - mass spectrometry (UHPLC MS) have been employed for metabolic profiling of cells exposed to a range of oxygen conditions. Additionally, time-of-flight secondary ion mass spectrometry (ToF SIMS) has been employed for imaging mass spectrometric analysis of multicellular tumour spheroids cultured from wild type cells and cells with dysfunctional HIF-1 to represent small initiating tumours. Using these techniques in metabolic profiling it has been possible to reveal metabolites associated with the effect of oxygen and HIF-1 on cancer metabolism along with key pathways and hubs that could be targeted in future therapy. Using imaging mass spectrometry it has been possible to localise metabolites in situ revealing how tumour structure relates to function. Finally, a novel approach to consider how metabolites are correlated with one another in the response to oxygen level or presence or absence of functional HIF-1 has been undertaken to better understand the systems properties of cancer metabolism. Metabolites found to be differently correlated with respect to oxygen and/or HIF-1 have been mapped onto a human metabolic network to determine their network-based origins. This allowed the simulation of…

Subjects/Keywords: 616.994; Cancer; Systems Biology; Metabolomics; Mass Spectrometry

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APA (6^th Edition):

Armitage, E. G. (2012). Systems biology of HIF metabolism in cancer. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/systems-biology-of-hif-metabolism-in-cancer(e237aa18-81a9-4c86-81b1-804555d3585c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559340

Chicago Manual of Style (16^th Edition):

Armitage, Emily Grace. “Systems biology of HIF metabolism in cancer.” 2012. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/systems-biology-of-hif-metabolism-in-cancer(e237aa18-81a9-4c86-81b1-804555d3585c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559340.

MLA Handbook (7^th Edition):

Armitage, Emily Grace. “Systems biology of HIF metabolism in cancer.” 2012. Web. 09 Dec 2019.

Vancouver:

Armitage EG. Systems biology of HIF metabolism in cancer. [Internet] [Doctoral dissertation]. University of Manchester; 2012. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/systems-biology-of-hif-metabolism-in-cancer(e237aa18-81a9-4c86-81b1-804555d3585c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559340.

Council of Science Editors:

Armitage EG. Systems biology of HIF metabolism in cancer. [Doctoral Dissertation]. University of Manchester; 2012. Available from: https://www.research.manchester.ac.uk/portal/en/theses/systems-biology-of-hif-metabolism-in-cancer(e237aa18-81a9-4c86-81b1-804555d3585c).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559340

University of Manchester

28. Maddison, Louise Elizabeth. Experimental and Theoretical Modelling of the MAPK Pathway.

Degree: 2012, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:167012

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The MAPK pathway plays a crucial role in regulating cellular response to external stimuli. Binding of growth factors and other mitogenic signals to cell surface… (more)

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The MAPK pathway plays a crucial role in regulating cellular response to external stimuli. Binding of growth factors and other mitogenic signals to cell surface receptors initiates a phosphorylation-dependent relay of protein activation, resulting in altered transcription, ultimately regulating cell proliferation and differentiation. Signalling through this pathway is regulated by the coordinated function of specific protein kinases and protein phosphatases. As perturbation of this signalling system is often associated with diseases such as cancer, modelling is a useful means to help understand the outcomes that may result following changes in component levels or activity. The determination of absolute quantification data, in copies per cell, for proteins of the MAPK pathway will allow the expansion of and improved accuracy within predictive models.The strategy used within this thesis is based on the established technique of stable isotope dilution, generating isotopically labelled peptides using the QconCAT methodology. Recombinant DNA techniques were used to generate artificial concatamers of large numbers of tryptic peptides as quantification standards. A QconCAT, LM1, of 49 KDa (29 tryptic peptides), corresponding to the scaffold proteins was designed and built to encode two peptides per protein. A second QconCAT, LM2, of 58 KDa (34 tryptic peptides), encoded peptides from the dual-specificity phosphatases (DUSPs) and substrates. Quantification was performed using ultra performance liquid chromatography coupled to mass spectrometry. A selected reaction monitoring (SRM) approach was employed where the most intense y-ions per peptide were selected either from experimental data or predictions in silico. Using the ratio of the signal for the light:heavy isotopologues, the amount of light isotopologue can be inferred, allowing copies per cell quantifications to be established. Native peptides were present below the lower limit of quantification, and therefore the upper bounds of copies per cell were obtained for the three cell lines; colon cancer cells HCT 116 (K-Ras mutant) and HT-29 (B-Raf mutant) and a control cell line of HEK-293. Finally, mathematical modelling was undertaken to explore the mass-action kinetics of a three component scaffold signalling molecule. It was found that the optimal scaffold concentration is between the lowest and second lowest concentration of signalling protein.

An emerging research field, known as Systems Biology, has the potential to provide a vital link to new drug discoveries to combat cancer. Systems Biology combines laboratory results and specialised software to simulate human cells in the computer. By working with these virtual cells, new insights into the disease can be revealed. Cells communicate to each other across a complex network of protein to protein interactions. When a small molecule known as a growth factor attaches to the outside of the cell, a relay of signals is stimulated. These signals travel through the cell to reach the nucleus. The nucleus holds the genetic…

Advisors/Committee Members: WESTERHOFF, HANS HV, Eyers, Claire, Westerhoff, Hans.

Subjects/Keywords: MAPK; Systems Biology; Mathematical Modelling; Mass Spectrometry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Maddison, L. E. (2012). Experimental and Theoretical Modelling of the MAPK Pathway. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:167012

Chicago Manual of Style (16^th Edition):

Maddison, Louise Elizabeth. “Experimental and Theoretical Modelling of the MAPK Pathway.” 2012. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:167012.

MLA Handbook (7^th Edition):

Maddison, Louise Elizabeth. “Experimental and Theoretical Modelling of the MAPK Pathway.” 2012. Web. 09 Dec 2019.

Vancouver:

Maddison LE. Experimental and Theoretical Modelling of the MAPK Pathway. [Internet] [Doctoral dissertation]. University of Manchester; 2012. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:167012.

Council of Science Editors:

Maddison LE. Experimental and Theoretical Modelling of the MAPK Pathway. [Doctoral Dissertation]. University of Manchester; 2012. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:167012

University of Manchester

29. Henderson, Fiona. Mass spectrometry imaging of lipid profiles in disease.

Degree: PhD, 2017, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometry-imaging-of-lipid-profiles-in-disease(f1b202b1-2a6e-416e-ab81-321ef4f0e24d).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740313

► It is well established that lipids play an important role in diseases such as non-alcoholic fatty liver disease and cardiovascular diseases. However, in the past… (more)

▼ It is well established that lipids play an important role in diseases such as non-alcoholic fatty liver disease and cardiovascular diseases. However, in the past decade, it has come to light that lipids may be important in other diseases; particularly in cancer and neurological disorders. Here, lipid metabolism has been investigated using pre-clinical cancer models for melanoma, glioma, non-small-cell lung cancer and colorectal cancer. The role of lipids in the recovery post-stroke has also been studied. Mass spectrometry imaging offers an ideal tool to study lipids in tissue ex-vivo. Lipids ionise well in a number of mass spectrometry modalities, and hundreds of lipids can be imaged in one mass spectrometry imaging experiment. Furthermore, mass spectrometry imaging offers excellent spatial resolution. In this work, both MALDI-MS and DESI-MS have been used for mass spectrometry imaging. Tumour lipid heterogeneity has been a particular focus of this this project. Heterogeneity exists within tumours, as well as between tumours in the same patient; and this causes major problems for therapy. Owing to the untargeted nature, and high spatial resolution of mass spectrometry imaging, it is an excellent technique to study lipid heterogeneity. Adjacent sections (or in some cases the same section used for mass spectrometry imaging), were used for immunofluorescence and H&E staining. By comparing mass spectrometry images with staining techniques, biological reasons for lipid heterogeneity can be established. Here, a particular focus has been on hypoxia (low oxygen tensions), which is a key contributor to tumour heterogeneity, and is associated with aggressive cancers. Additionally, hypoxia is a feature of ischaemic stroke, and lipids in ischaemic stroke have also been investigated. PET is a non-invasive imaging technique which is able to image a radiolabelled molecule (tracer) in the body. Here, PET has been used as a complementary in-vivo technique to mass spectrometry imaging. The tracers [11C] acetate and [18F]-FTHA have been used to image fatty acid synthase and fatty acid uptake in tumours; both of which are hypothesised to be key in cancer progression. REIMS is a newly established mass spectrometry technique. It is ideal for analysing lipids in cells, as sample preparation is minimal. Here, approaches for cell pellet analysis have been tested, and used to detect lipids in cancer cell lines.

Subjects/Keywords: 610; Cancer; Mass spectrometry imaging; Lipids

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Henderson, F. (2017). Mass spectrometry imaging of lipid profiles in disease. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometry-imaging-of-lipid-profiles-in-disease(f1b202b1-2a6e-416e-ab81-321ef4f0e24d).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740313

Chicago Manual of Style (16^th Edition):

Henderson, Fiona. “Mass spectrometry imaging of lipid profiles in disease.” 2017. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometry-imaging-of-lipid-profiles-in-disease(f1b202b1-2a6e-416e-ab81-321ef4f0e24d).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740313.

MLA Handbook (7^th Edition):

Henderson, Fiona. “Mass spectrometry imaging of lipid profiles in disease.” 2017. Web. 09 Dec 2019.

Vancouver:

Henderson F. Mass spectrometry imaging of lipid profiles in disease. [Internet] [Doctoral dissertation]. University of Manchester; 2017. [cited 2019 Dec 09]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometry-imaging-of-lipid-profiles-in-disease(f1b202b1-2a6e-416e-ab81-321ef4f0e24d).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740313.

Council of Science Editors:

Henderson F. Mass spectrometry imaging of lipid profiles in disease. [Doctoral Dissertation]. University of Manchester; 2017. Available from: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometry-imaging-of-lipid-profiles-in-disease(f1b202b1-2a6e-416e-ab81-321ef4f0e24d).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740313

University of Manchester

30. Upton, Alice. Characterising Antibody Conformation and Glycosylation using Mass Spectrometry Techniques.

Degree: 2019, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318323

► Monoclonal antibody (mAb)-based therapeutics are dominating the pharmaceutical market for the targeted treatment of a wide range of diseases. With this market dominance comes an… (more)

▼ Monoclonal antibody (mAb)-based therapeutics are dominating the pharmaceutical market for the targeted treatment of a wide range of diseases. With this market dominance comes an increase in competition from the market manufacturers who want a share of the ~$100 billion world-wide sales. As originator products come off patent the opportunity opens up for other manufacturers to step-in and develop a biosimilar (biologically equivalent) product. However, rigorous biosimilarity testing is required before such products can be approved for clinical use. In order to define acceptance criteria for any biosimilar candidate, a full characterisation of multiple originator products must be completed. The use of mammalian cell lines during the manufacturing process; however, can lead to an inherently heterogeneous mAb product, making biosimilarity approval a non-trivial process. The presence of Post-Translational Modifications (PTMs) such as glycosylation, are essential for the therapeutic efficacy of many mAb products and therefore the glycan profiles must be identified and quantified in full. Mass Spectrometry (MS) has evolved into an important tool for studying the critical quality attributes of mAbs thanks to low sample consumption, high sensitivity and high throughput. Combined with Ion Mobility separation (IM-MS), the range of conformational ensembles adopted by different proteins can also be studied. The rotationally averaged Collision Cross Section (CCS) of a protein is indicative of its structural diversity and hierarchy. In addition, the solution-phase labelling technique, Hydrogen-Deuterium Exchange (HDX), can be coupled with MS for the study of conformational dynamics. These three techniques (MS, IM-MS and HDX-MS) are used extensively throughout this thesis to assess lot-to-lot variation between Herceptin mAb products. A â€˜LCâ€™-MS method combined with enzymatic digestions was developed for the rapid identification and quantification of glycan profiles and for the determination of glycan occupancy and high mannose content. These results were coupled with orthogonal techniques to link afucosylation to therapeutic efficacy. IM-MS and HDX-MS were used to simultaneously assess lot-to-lot variations and the effects of glycosylation in terms of the conformational spread and dynamic properties of Herceptin. The use of activated IM-MS offered insights into the stabilisation induced by the glycans. Finally, IM-MS and Variable Temperature (VT) IM-MS was used to probe the effects of cold storage upon the conformational flexibility of mAbs. Initial findings suggested a significant restriction upon the global framework of Herceptin following storage at -80 Â°C cf. storage at 4 Â°C. Advisors/Committee Members: KNIGHT, DAVID D, Barran, Perdita, Knight, David.

Subjects/Keywords: Antibody; Biosimilar; Mass Spectrometry; Ion Mobility; Glycosylation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Upton, A. (2019). Characterising Antibody Conformation and Glycosylation using Mass Spectrometry Techniques. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318323

Chicago Manual of Style (16^th Edition):

Upton, Alice. “Characterising Antibody Conformation and Glycosylation using Mass Spectrometry Techniques.” 2019. Doctoral Dissertation, University of Manchester. Accessed December 09, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318323.

MLA Handbook (7^th Edition):

Upton, Alice. “Characterising Antibody Conformation and Glycosylation using Mass Spectrometry Techniques.” 2019. Web. 09 Dec 2019.

Vancouver:

Upton A. Characterising Antibody Conformation and Glycosylation using Mass Spectrometry Techniques. [Internet] [Doctoral dissertation]. University of Manchester; 2019. [cited 2019 Dec 09]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318323.

Council of Science Editors:

Upton A. Characterising Antibody Conformation and Glycosylation using Mass Spectrometry Techniques. [Doctoral Dissertation]. University of Manchester; 2019. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318323

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