MSc Precision Medicine / Course details

Year of entry: 2024

Course unit details:
Proteomics and Metabolomics

Course unit fact file
Unit code BIOL72031
Credit rating 15
Unit level FHEQ level 7 – master's degree or fourth year of an integrated master's degree
Teaching period(s) Semester 1
Available as a free choice unit? No

Overview

The unit will focus on the profiling and targeted analysis of proteins and metabolites in biological systems. The unit aims to provide students with an introduction to the scientific disciplines of proteomics and metabolomics and how relevant experimental techniques are applied in medical research with an emphasis on biomarker discovery and applications in diagnosis and prognosis of disease. The unit covers experimental techniques for measurement; protein localization; quantitative assays; in vitro or in vivo studies of protein structure, function, and post-translational modification; metabolic pathway enrichment analyses and overview of data handling as well as analysis. The teaching of proteomics and metabolomics will be interspersed across a two-three week period.

Aims

The primary objective of this module is to introduce the scientific disciplines of proteomics and metabolomics. The secondary objective is to provide an appreciation of the experimental techniques used in proteomic and metabolomic studies. Students will gain knowledge of basic requirements for proteomic and metabolomic studies and insights into how these techniques are applied in medical research with emphasis on biomarker discovery and applications in diagnosis of disease. The unit will provide overview of entire workflows of both omics technologies.

Learning outcomes

Knowledge and understanding 
Students should be able to: 

(i)    Identify and recall different proteomics and metabolomics approaches for biomarker discovery.
(ii)    Explain the working principles of key analytical techniques used in metabolomics and proteomics.
(iii)    Summarize the diagnostic platforms utilized for measuring proteins and metabolites in Precision Medicine.
(iv)    Analyse and evaluate the design of metabolomic and proteomic experiments in a critical manner.
(v)    Assess and determine the relevance of omics results in published biomedical research.


Intellectual skills 
Students should be able to:

(vi)    Assess and critique current Proteomics and Metabolomics research in Precision Medicine from a critical perspective.
(vii)    Create and develop research questions pertaining to the utilization of proteomic and metabolomic techniques for the identification of biomarkers and characterization of molecular phenotypes in diseases.


Practical skills 
Students should be able to: 

(viii)    Apply effective communication skills to present scientific data in a clear, concise, and impactful manner through visual, oral, and written means.
(ix)    Analyse and interpret metabolomics and proteomics research data while identifying limitations within the study design.


Transferable skills and personal qualities 
Students should be able to: 

(x)    Apply effective communication skills in various forms and contexts to convey information clearly and accurately.
(xi)    Analyse complex problems, identify their components, and develop strategies to address and solve them effectively.
(xii)    Integrate independent thinking with collaborative skills to work effectively as a team member, contributing unique perspectives while also respecting and collaborating with others.

Teaching and learning methods

The module will be delivered over two-three weeks and consists of a series of face-to-face lectures, interactive seminars, omics lab tour and pre-recorded content. Lectures are supported with examples of online resources and/or key references. 
Enquiry-based learning will be applied to allow students to perform critical thinking in relation to scientific studies already performed and published in peer-reviewed journals. The group presentations provide further learning opportunities and formative feedback will be provided through seminar activities. A multiple-choice questions exam will test the fundamental understanding of topics covered.

Group presentation of omics journal article 30%
Written research proposal 30% 
MCQ exam 40% 

Knowledge and understanding

(i)    Identify and recall different proteomics and metabolomics approaches for biomarker discovery.
(ii)    Explain the working principles of key analytical techniques used in metabolomics and proteomics.
(iii)    Summarize the diagnostic platforms utilized for measuring proteins and metabolites in Precision Medicine.
(iv)    Analyse and evaluate the design of metabolomic and proteomic experiments in a critical manner.
(v)    Assess and determine the relevance of omics results in published biomedical research.

Intellectual skills

(vi)    Assess and critique current Proteomics and Metabolomics research in Precision Medicine from a critical perspective.
(vii)    Create and develop research questions pertaining to the utilization of proteomic and metabolomic techniques for the identification of biomarkers and characterization of molecular phenotypes in diseases.

Practical skills

(viii)    Apply effective communication skills to present scientific data in a clear, concise, and impactful manner through visual, oral, and written means.
(ix)    Analyse and interpret metabolomics and proteomics research data while identifying limitations within the study design.

Transferable skills and personal qualities

(x)    Apply effective communication skills in various forms and contexts to convey information clearly and accurately.
(xi)    Analyse complex problems, identify their components, and develop strategies to address and solve them effectively.
(xii)    Integrate independent thinking with collaborative skills to work effectively as a team member, contributing unique perspectives while also respecting and collaborating with others.

Assessment methods

Method Weight
Other 40%
Written assignment (inc essay) 30%
Oral assessment/presentation 30%

Group presentation of omics journal article 30%
Written research proposal 30% 
MCQ exam 40% 

Feedback methods

Marks and written feedback are provided to students on all written and oral assessments, including feedback on what was done well and what could be improved in order to achieve the next grade. 
A survey is used to gather feedback from the students on the course unit.

Recommended reading

Core text for metabolomics: Adamski J, Metabolomics for Biomedical Research (2020), Academic press, Available via library and as e-book.

Metabolomics 
1.    Bos LD, Sterk PJ, Fowler SJ. (2016), Breathomics in the setting of asthma and chronic obstructive pulmonary disease. J Allergy Clin Immunol 138:970-6 
2.    Goodacre, R. et al. (2004) Metabolomics by numbers - acquiring and understanding global metabolite data. Trends in Biotechnology 22, 245-252 
3.    Goodacre, R. (2007) Metabolomics of a superorganism. Journal of Nutrition 137, 259S 266S 
4.    Holmes et al. (2008). Metabolic phenotyping in health and disease. Cell 134:714-717. 
5.    Kell DB (2004). Metabolomics and systems biology: Making sense of the soup. Current Opinion in Microbiology 7(3):296-307 
6.    Lawal O et al (2017) Exhaled breath analysis: a review of 'breath-taking' methods for off-line analysis. Metabolomics 13:110. doi: 10.1007/s11306-017-1241-8 
7.    Mamas, M.,et al (2011) The role of metabolites and metabolomics in clinically applicable biomarkers of disease. Archives of Toxicology 85, 5- 17. 
8.    Trivedi, D. et al (2017) Metabolomics for the masses: the future of metabolomics in a personalised world. New Horizons in Translational Metabolomics 3(6):294-305 
9.    Wishart DS (2016). Emerging applications of metabolomics in drug discovery and precision medicine. Nature Rev. Drug. Discov. doi: 10.1038/nrd.2016.32. 

Proteomics:
10.    Aebersold R and Mann M. (2016) Mass-spectrometric exploration of proteome structure and function. Nature. 537(7620):347-55. 
11.    Chait BT. (2006) Mass spectrometry: bottom-up or top-down? Science. 314(5796):65-6. 
12.    Chen et al. (2012). Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148:1293-1307. 
13.    Domon B1, Aebersold R (2006), Mass spectrometry and protein analysis. Science. 312(5771):212-7. 
14.    Ebhardt HA, et al (2015) Applications of targeted proteomics in systems biology and translational medicine. Proteomics (18):3193-208. 
15.    Geyer PE et al. (2017) Revisiting biomarker discovery by plasma proteomics, Mol Syst Biol, 13(9): 942 
16.    Gahoi N1, Ray S, Srivastava S. (2015), Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges, Proteomics, 15(2-3): 218-31
17.    Latosinska A et al (2015), Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PLoS One.10(9): e0137048. 
18.    Marcotte EM. (2007), How do shotgun proteomics algorithms identify proteins? Nat Biotechnol; 25(7):755-7. 
19.    Rogowska-Wrzesinska A et al (2013), 2D gels still have a niche in proteomics. J Proteomics. 88:4-13. 
 

Study hours

Scheduled activity hours
Work based learning 30
Independent study hours
Independent study 120

Teaching staff

Staff member Role
Drupad Trivedi Unit coordinator

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