High Resolution Mass Spectrometer to support Proteomic Research across the Southern 4 Proteomic Consortium

Lead Research Organisation: University of Southampton
Department Name: School of Biological Sciences

Abstract

New instrumentation for increased capability in Proteomic Research

Proteins are a major building block of cells and perform a huge range of biological functions. Proteomics is the systematic study of the expression, functions and interactions of proteins.

The key techniques used in proteomics are mass spectrometry (MS) and liquid chromatography and are performed on instruments called Mass Spectrometers; and High Performance Liquid Chromatography (HPLC) systems. In combination, these two instruments are designed to separate and identify proteins, fragments of proteins (peptides) and modified proteins obtained from cells, tissues and biofluids. They allow us to compare the amounts of proteins between different conditions (e.g., comparison of protein levels between normal cells and cancer cells), and to identify proteins important within a specific biological process including normal ones and those important in human diseases. This application will support the purchase of an advanced Mass Spectrometer and HPLC system with an enhanced ability to measure the amounts of these proteins and peptides at very low levels and with high accuracy.

The instrumentation has been requested by the Southern 4 Proteomic Consortium and will form part of a Proteomics hub in the South of England that will allow several universities to use this state-of-the-art instrumentation. This consortium also provides a forum to exchange proteomic expertise and knowledge; and to train researchers in the latest proteomic techniques. Housed within the Centre for Proteomic Research at the University of Southampton, the increased capacity and advanced capabilities of this instrumentation will permit a wide range of proteomic studies within areas of strategic importance, including those within many BBSRC priority areas including healthy aging across the lifecourse; bioenergy, generating new replacement fuels for a greener, sustainable future; food, nutrition and health; sustainability enhancing agricultural production; systems approaches to the biosciences; synthetic biology and data-driven biology.

Technical Summary

Proteins are the ultimate effectors of almost all cellular processes. As such, there is a requirement for biological systems to be explained in terms of the levels, interactions, regulation and modifications of proteins - which are the capabilities of proteomics. The requested instruments are a new high-resolution hybrid Mass Spectrometer (MS) and nanoscale Ultra High Performance Liquid Chromatography system to support cutting-edge proteomic research across multiple institutions in the South of England as part of a Southern Proteomics Consortium (S4PC).

This state-of-the-art instrumentation will provide a step-change in Proteomic research, allowing investigators to perform in-depth and innovative proteomic studies regardless of the biological system under investigation, bringing an increase in both capability and capacity to perform large-scale experiments using label-free and stable isotope-labelling strategies, provide sensitive targeted quantitative proteomics and a substantially improved ability to characterize post-translational modifications. These new capabilities will allow researchers to tackle important new research questions, many of which are within the BBSRCs strategic priority areas. Importantly, the latest generation of MS instruments has improved performance characteristics (enhanced mass accuracy, resolution, modes of acquisition and sensitivity), which will increase both the quality and quantity of proteomic data that can be obtained. This investment will also have a major impact on the proteomic technology that our external academic and industrial collaborators of the S4PC institutions have access to, extending the range and quality of research that can be performed.

Planned Impact

The requested instrumentation will provide proteomic capability to researchers across the Southern 4 Proteomics Consortium with applicants representing academic departments in Biosciences, Oceanography, Chemistry; and Health and Medical Sciences, illustrating the broad impact of the research proposed. The new instrumentation will also provide ample opportunities for strengthening current collaborations and forging new links with other institutions and industry.

The research proposed is relevant to important world issues such as environmental change, food security, bioenergy, healthy ageing, as well as providing high-class bioscience underpinning many important health-care issues. The work undertaken in the individual projects will also have impact within those research areas.

C. Proud's research is important for academic researchers and industrial partners, who are interested in eEF2K or the Mnks as therapeutic targets in diseases such as cancers. A better knowledge of the normal functions of these kinases and pathways will aid understanding of their roles in animal physiology and healthy ageing, thus ultimately benefiting the pharmaceutical industry, the healthcare sector and the wider community.

M. Terry's research focuses on how the photosynthetic apparatus in plants is assembled in the early stages of seedling development. This research will benefit those working in the areas of chloroplast-nucleus signaling/biogenesis, photosynthesis, and stress signaling. It is relevant to industrial partners/other organizations designing crop plants to increase productivity and the wider public as it addresses important issues related to the food security/bioenergy debate.

R. Ewing's research focuses on identifying new interacting proteins in signaling complexes or networks that are rewired in disease. This research will benefit researchers interested in interaction proteomics and signal transduction pathways, particularly in cancer, an important factor in the ageing population, as well as industrial partners interested in new therapeutic targets, the healthcare sector, patient communities and the wider public, where cancer can have a major impact on their lives.

T. Bibby's research is focused on the ability to engineer photosynthetic cells from marine algae to maximise their energy efficiency for conversion into useful biofuels/bioproducts. This research is therefore important for academics and industry interested in using marine algae for synthetic biology and bioenergy research.

R. Cramer Medicinal plants and their natural products are a potent source of new drug compounds and disease therapies. Novel data revealing location-specific protein expression in an important medicinal plant provides essential information for elucidation and isolation of medically and economically valuable plant metabolites. These are of major interest to the pharmaceutical industry, the healthcare sector and the wider public.

B. Moore's research focuses on the mechanisms involved in lipid loading in human hepatocytes. Disruption of nutrient metabolism and energy homeostasis in the liver leads to conditions such as obesity and type 2 diabetes, all of which prevent healthy aging. The identification of rationalised strategies to protect the liver from fat accumulation would be of major interest to the Foods and Pharmaceutical industry and have a huge impact on the public health and well-being of the UK population, and would in the longer term reduce the cost burden of UK healthcare.

G. Kneale's research into R-M controller proteins will advance our understanding of the fundamental mechanisms of gene regulation in bacteria, and provide new insights into novel mechanisms of DNA sequence recognition by gene regulatory proteins. An understanding of these mechanisms will be benefit medical microbiologists and the pharmaceutical industry in providing new targets for novel anti-bacterial drug development.

Publications

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Burg D (2018) Large-Scale Label-Free Quantitative Mapping of the Sputum Proteome. in Journal of proteome research

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Parkinson E (2018) Determination of Protein Haptenation by Chemical Sensitizers Within the Complexity of the Human Skin Proteome. in Toxicological sciences : an official journal of the Society of Toxicology

 
Description This award was to fund a high-resolution mass spectrometer to improve the infrastructure within the Southern-4-Proteomics Consortium, allowing in-depth proteomic analyses to be performed. As such the instrumentation is supporting a wide range of research projects (~9 million GBP fof funded research). As an example a major discovery that the instrumentation has been key in supporting is an EU funded Innovative Medicines Initiative programme in Severe Asthma, where by using this instrumentation, we have defined 10 new disease phenotypes of severe asthma using proteomic data integrated with clinical data. We have defined protein biomarkers for each of these phenotypes, and identified specific mechanistic pathways underlying each (3 manuscripts currently in review) Using this information we are currently operating a clinical trial with major pharma, evaluating the response of these phenotypes to current drug therapy. A programme of research funded on the basis that we had the capability in terms of expertise and the instrumentation funded by this award, is currently underway, performing deep molecular phenotyping of tumour samples from patients (proteomics, immunopeptidomics, transcriptomics, bioinformatics) to identify neoantigens as part of a pipeline to develop rapid personalised vaccines for Melanoma, Head and Neck cancer and Lung cancer. Using this instrumentation, and the deveoped immunopeptidomics capability, we have identified chemical sensitiser specific immunopeptides presented by cells within skin, which is facilitating the development of an in-silico model to allow future safety risk assessment of the sensitisation potential of new chemicals used in consumer products (1 paper published, 2 manuscripts in preparation)
Exploitation Route The discovery of these new molecular phenotypes, accommpanying clinical features and biomarkers improves our understanding of the different molecular mechanisms underpinning the disease. It will also allow the development and re-purposing of therapies to an individual or group of patients, providing the right therapy, to the right patient at the right time. Building upon this research grant and the IMI research, a clinical trial is currently underway with Novartis is currently underway assessing the efficacy of the current drug Xolair, using the biomarkers defining these phenotypes to identify responders and non-responders to treatment.
Sectors Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Current and significant non-academic impacts using this instrumentation include: 1.The discovery of novel molecular phenotypes of severe asthma which will lead to more effective patient treatment. 2. The development of advanced techniques and approaches to characterise the immunpeptidomes which are a key component of the pathway leading to the direct development of personalised vaccines. 3. Identification of sensitiser exposure specific immunopeptides, comprehensive protein turnover and protein expression data is currently faciltating the development of in- silico models to enable risk evaluation of the sensitising capacity of new chemical formulations, replacing the use of animals.
First Year Of Impact 2017
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic

 
Description MRC Discovery Award: Maths, Engineering and Life Sciences: making connections for precision medicine (2017)
Amount £6,843 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 11/2017 
End 11/2018
 
Description Novartis Principal investigator led research grant
Amount £3,960,000 (GBP)
Organisation Novartis 
Sector Private
Country Global
Start 09/2016 
End 09/2019
 
Description Towards new therapeutic strategies: Zika-driven oncolysis of brain tumor cells
Amount £183,000 (GBP)
Funding ID MR/S01411X/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 11/2018 
End 10/2020
 
Description Unilever - Principal investigator led grant - LOPITSENSE
Amount £120,000 (GBP)
Organisation Unilever 
Department Unilever Research and Development
Sector Private
Country United Kingdom
Start 04/2016 
End 04/2017
 
Description Unilever - principal investigator led research programme
Amount £610,000 (GBP)
Organisation Unilever 
Department Unilever Research and Development
Sector Private
Country United Kingdom
Start 07/2015 
End 06/2018
 
Description University of Southampton, Biological Sciences PhD studentship award
Amount £45,000 (GBP)
Organisation University of Southampton 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 09/2021
 
Description Wessex Medical Research PhD studentship
Amount £91,000 (GBP)
Organisation Wessex Medical Research 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2015 
End 09/2018
 
Description Cancer Research UK accelerator award - Tumour phenotyping 
Organisation University of Oxford
Department Nuffield Department of Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution The partnership establishes a multi-­disciplinary immunotherapy collaboration with leading expertise in immunology, oncology, genomics, molecular pathology ,immunoproteomics, bioinformatics and drug development. The aim is to: Characterise the evolving Tumour antigenic landscape utilising mutanome, proteome and immunopeptidome analysis (combining ex-Vivo and in silico methods) pre and post treatment. Determine the phenotype and transcriptional profile of tumour infiltrating immune cells at population and single cell levels utilising multidimensional flow cytometry and RNAseq, linked to immunohistochemistry. Determine TCR repertoire depth by targeted mapping analysis of single-.cell RNA-.Seq data from tumour infiltrating cells, and link it to tumour mutanome profiling to identify antigens, TCRs and/or T cell clonotypes that are likely to provide robust anti tumour immune responses following vaccination or adoptive T cell therapy. Use advanced bioinformatics define predictive biomarkers for response/toxicity from the resulting data and in readiness for prospective validation in clinical trials. We have now transfered the expertise of mass spectrometry based immunopeptidomics at Oxford to Southampton and have established a world class immunopeptidomics pipeline which is currently performing in depth analysis of tumour tissues to define the antigenic tumour landscape.
Collaborator Contribution The partnership establishes a multi-­disciplinary immunotherapy collaboration with leading expertise in immunology, oncology, genomics, molecular pathology ,immunoproteomics, bioinformatics and drug development (as above since the project has just been made active)
Impact We have now transfered the expertise of mass spectrometry based immunopeptidomics at Oxford to Southampton and have established a world class immunopeptidomics pipeline which is currently performing in depth analysis of tumour tissues to define the antigenic tumour landscape. Work is still ongoing
Start Year 2017
 
Description Southern 4 Proteomics Consortium 
Organisation University of Portsmouth
Country United Kingdom 
Sector Academic/University 
PI Contribution We have developed a collaborative framework across the Southern region with the Universities of Southampton, Surrey, Reading and Portsmouth (Southern 4 Proteomics Consortium, S4PC) to share expertise and knowledge in proteomic research. Through BBSRC funding, these institutions now have shared access to state of the art proteomic instrumentation housed within the University of Southampton. We have organised and hosted a number of proteomic training workshops, where researchers are taught how to use the latest generation of high-resolution mass spectrometer and data analysis software
Collaborator Contribution Researchers from these institutions have shared their proteomic knowledge and expertise with other members of the consortium
Impact As a consortium, we have provided three proteomic training workshops hosted at the University of Southampton for researchers across the four institutions, training them in the latest proteomic techniques and competency in the operation of the latest mass spectrometry instrumentation and software.
Start Year 2014
 
Description Southern 4 Proteomics Consortium 
Organisation University of Reading
Department School of Chemistry, Food and Pharmacy
Country United Kingdom 
Sector Academic/University 
PI Contribution We have developed a collaborative framework across the Southern region with the Universities of Southampton, Surrey, Reading and Portsmouth (Southern 4 Proteomics Consortium, S4PC) to share expertise and knowledge in proteomic research. Through BBSRC funding, these institutions now have shared access to state of the art proteomic instrumentation housed within the University of Southampton. We have organised and hosted a number of proteomic training workshops, where researchers are taught how to use the latest generation of high-resolution mass spectrometer and data analysis software
Collaborator Contribution Researchers from these institutions have shared their proteomic knowledge and expertise with other members of the consortium
Impact As a consortium, we have provided three proteomic training workshops hosted at the University of Southampton for researchers across the four institutions, training them in the latest proteomic techniques and competency in the operation of the latest mass spectrometry instrumentation and software.
Start Year 2014
 
Description Southern 4 Proteomics Consortium 
Organisation University of Surrey
Country United Kingdom 
Sector Academic/University 
PI Contribution We have developed a collaborative framework across the Southern region with the Universities of Southampton, Surrey, Reading and Portsmouth (Southern 4 Proteomics Consortium, S4PC) to share expertise and knowledge in proteomic research. Through BBSRC funding, these institutions now have shared access to state of the art proteomic instrumentation housed within the University of Southampton. We have organised and hosted a number of proteomic training workshops, where researchers are taught how to use the latest generation of high-resolution mass spectrometer and data analysis software
Collaborator Contribution Researchers from these institutions have shared their proteomic knowledge and expertise with other members of the consortium
Impact As a consortium, we have provided three proteomic training workshops hosted at the University of Southampton for researchers across the four institutions, training them in the latest proteomic techniques and competency in the operation of the latest mass spectrometry instrumentation and software.
Start Year 2014
 
Description EMBL-EBI Industry Programme workshop: Bio-pharmaceutical opportunities in proteomics, EMBL-EBI, Hinxton, UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Dr Robert Ewing was invited to give a talk on Protein networks and cancer signalling to promote/facilitate the discussion during the workshop
Year(s) Of Engagement Activity 2017
 
Description Human Proteome Organisation (HUPO) annual international conference - Dublin - Liquid Biopsy Session - The Shape of Asthma - Invited speaker - Dr Paul Skipp 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The working group discussed the use of liquid biopsies and their use for biomarker discovery and the best practices to translate these findings to the clinic for patient benefit. It was agreed that a joint positioning paper/review would be published in collaboration with the working group members.
Year(s) Of Engagement Activity 2017
 
Description Keynote presentation by Dr Robert Ewing on the Networks and Pathways course, EBI, Hinxton, UK 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Kenote speaker on the Networks and Pathways course, EBI, Hinxton, UK. The was good engagement from course participants regarding learning approaches and techniques to studying protein-protein interactions.
Year(s) Of Engagement Activity 2017
 
Description Lecture at 12th International Agean conference on Pathways, Networks and Systems Medicine by Dr Robert Ewing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Lecture at 12th International Agean conference on Pathways, Networks and Systems Medicine. This sparked a number of discussions after the talk with fellow academics
Year(s) Of Engagement Activity 2017
 
Description Lecture at Human Proteome Organisation annual conference, Dublin by Dr Robert Ewing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dissemination of latest research on Oncogenic Wnt/Beta -catenin signalling network analysis using multi-omics in colorectal cancer
Year(s) Of Engagement Activity 2017
 
Description Lecture by Dr Paul Skipp at Astra Zeneca on Label Free Proteomics: A New DIA Strategy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Presentation on a new label-free proteomic acquisition approach and its application to skin sensitisation. Through discussions after the talk, there were a number of discusions concerning both the new acquisition technique and biological findings.
Year(s) Of Engagement Activity 2017
 
Description Lecture by Dr Robert Ewing at UCB Pharma, Slough, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Lecture on Signalling networks and protein interaction networks. Currently in discussions concerning further related work and collaborative opportunities
Year(s) Of Engagement Activity 2017
 
Description Lecture by Dr Robert Ewing at the Instituto de Biociencias, Univerdidade de Sao Paulo 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation on Cancer signalling and protein interaction networks. This has generated a number of discussions with current collaborators at the institution concerning future collaborative projects.
Year(s) Of Engagement Activity 2017
 
Description The Shape of Severe Asthma 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Research talk communicating the results of an EU Innovative Medicnes Initiative UBIOPRED to ~150 academics in the area of Proteomics - by Dr Paul Skipp
Year(s) Of Engagement Activity 2018
 
Description Video for describing research using a new acquisition strategy devloped by the manufacturer Waters 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Provided a video blog for Waters corporation on research my group had performed using the new mass spectrometry acquisition strategy SONAR.
Year(s) Of Engagement Activity 2018
URL https://www.youtube.com/watch?v=4rGYBOc-MEE