High Resolution Mass Spectrometer to support Proteomic Research across the Southern 4 Proteomic Consortium
Lead Research Organisation:
University of Southampton
Department Name: Centre for 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.
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.
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.
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
Bailey A
(2021)
Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells
in Toxicological Sciences
Bowler EH
(2019)
Proteomic Analysis of Azacitidine-Induced Degradation Profiles Identifies Multiple Chromatin and Epigenetic Regulators Including Uhrf1 and Dnmt1 as Sensitive to Azacitidine.
in Journal of proteome research
Burg D
(2018)
Large-Scale Label-Free Quantitative Mapping of the Sputum Proteome.
in Journal of proteome research
Conforti F
(2020)
Paracrine SPARC signaling dysregulates alveolar epithelial barrier integrity and function in lung fibrosis.
in Cell death discovery
Cruz AA
(2020)
Asthma similarities across ProAR (Brazil) and U-BIOPRED (Europe) adult cohorts of contrasting locations, ethnicity and socioeconomic status.
in Respiratory medicine
De Meulder B
(2018)
A computational framework for complex disease stratification from multiple large-scale datasets.
in BMC systems biology
Ewing RM
(2018)
Multiproteomic and Transcriptomic Analysis of Oncogenic ß-Catenin Molecular Networks.
in Journal of proteome research
Frapwell CJ
(2020)
Antimicrobial Activity of the Quinoline Derivative HT61 against Staphylococcus aureus Biofilms.
in Antimicrobial agents and chemotherapy
Gastaldello A
(2021)
The immunopeptidomes of two transmissible cancers and their host have a common, dominant peptide motif.
in Immunology
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 | 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 | ABC Discover |
Amount | £1,285,000 (GBP) |
Funding ID | ABC Discover_Skipp |
Organisation | Against Breast Cancer |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2019 |
End | 06/2024 |
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 | Public |
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 | 08/2016 |
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 | Public |
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 | 03/2016 |
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 | 06/2015 |
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 | 09/2018 |
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 | 09/2015 |
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 |