91572 Proteomics
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Subject handbook information prior to 2024 is available in the Archives.
Credit points: 8 cp
Result type: Grade and marks
There are course requisites for this subject. See access conditions.
Anti-requisite(s): 91536 Proteomics AND 91575 Proteomics
Description
Proteomics describes the study of the complete set of proteins (proteome) that is expressed at a given time in a cell, tissue, organ or organism. Modern proteomics involves the integration of a wide range of analytical tools and bioinformatics to identify qualitative and quantitative changes in proteins and specifically proteoforms; for example, in the detection of altered protein abundance associated with a disease. This subject covers leading and emerging technologies for sample preparation, protein fractionation, separation, mass spectrometry and data analysis for protein identification and characterisation.
This subject uses the field of proteomics to challenge student’s critical thinking skills and open their eyes to the need for an enquiring mindset that engages in unbiased thinking, learning how to use the information presented to them and their own knowledge to make intelligent decisions. Students explore critical thinking through examining facets of experimental design and data analysis through self-directed learning tasks and facilitated workshop activities. They are introduced to the best practice sample preparation technologies for different sample types, such as micro-organisms, plants, mammalian tissue and fluids. Written and oral assessment tasks require students to undertake independent research of relevant literature. The practical component allows students, through practice-related learning, to understand the logic and methodology underpinning sample preparation, complex mixture fractionation, protein separations and mass spectrometry. Students demonstrate their practice-related learning through the completion of a small laboratory-based project which requires a publication-style report encompassing data analysis skills.
Subject learning objectives (SLOs)
Upon successful completion of this subject students should be able to:
| 1. | Articulate how proteomics fits into the broader picture of systems biology, biological research and medical biotechnology. |
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| 2. | Plan an experiment using appropriate methods; taking into account the constraints of the available technology, sample numbers and amounts, and the underlying hypothesis. |
| 3. | Perform basic sample preparation on cellular and fluid samples, protein separation by 1-D electrophoresis, sample preparation for liquid chromatography-mass spectrometry and basic data analysis. |
| 4. | Collect, review and critically analyse published proteomics research and methodological literature. |
| 5. | Synthesise the collected data and supporting literature into a report that describes how the proteome of an organism can undergo biological changes due to a change in its environmental conditions. |
Course intended learning outcomes (CILOs)
This subject also contributes specifically to the development of following course intended learning outcomes:
- Critically appraise and apply advanced knowledge and technical skills to discipline specific projects to inform professional practice in science and medical biotechnology. (1.1)
- Assess, argue for, and conduct independent research and solving complex problems by applying a research methodology to address a research need in a relevant professional context. (2.1)
- Develop, prepare, and engage, at times collaboratively, in safe, ethical, organised and transparent work practices that mitigate risk and contribute to solving global health problems in the context of science and medical biotechnology. (3.1)
- Reflectively discover, create, and evaluate processes used to determine the value, integrity, and relevance of multiple sources of information to derive innovative solutions to complex science and medical biotechnology problems. (4.1)
- Present and communicate complex ideas and justifications using appropriate communication approaches from a variety of methods (oral, written, visual) to communicate with discipline experts, scientists, industry, and the general public. (5.1)
- Critically reflect on Indigenous Australian contexts to inform professional cultural capability to work effectively with and for, Indigenous Australians within Science and medical biotechnology. (6.1)
Contribution to the development of graduate attributes
1.Disciplinary knowledge
You will gain an understanding of the principles and practical uses of proteomics and the current technology platforms available to perform analysis of proteins, peptides and their modifications. You will be able to design a quantitative experiment that measures changes in proteoform abundance, one that combines current methodologies to create a workflow that is ‘fit for the purpose’ required. In addition, you will have an understanding of how proteomics fits into the broader picture of systems biology and biological research.
2. Research, inquiry and critical thinking
You will have the opportunity to apply critical and independent thinking to the planning of experiments using a wide range of methods to generate relevant data answering a specific scientific question. You will also learn how to find and interpret theoretical knowledge and practiced methodologies from a wide range of sources such as published literature, online databases and the course content, applying an understanding of recent developments in the discipline.
You will have the opportunity to learn to use different sources and types of information to interpret experimental data and contextualize it in the broader scope of the field, adding depth and significance to data analysis through the use of peer-reviewed publications, databases, research and review articles, textbooks, catalogues and technical reference books.
3.Professional, ethical and social responsibility
You will have an opportunity to develop professional-level competency in basic hands-on proteomics methods and data analysis. In addition, technical and creative skills will be developed to investigate, analyse and synthesise complex information, problems, concepts and theories. You will then apply these skills to examine and criticise established theories. Finally, you will practise the integration of proteomics data within the scope of broader systems biology and medical research programs.
You will have an opportunity to develop skills in the management of the work-load required for scientific-based practice and professional work. Time management will be developed through strictly time-limited practical and tutorial sessions.
4. Reflection, Innovation, Creativity
You will be encouraged, through the use of examples and case studies, to view proteomics and science in general as a two-way street where basic research informs clinical activity and vice versa. Through reflective tasks that will enhance your understanding of the technologies, you will be shown the need in proteomics to be innovative in chosen experimental approaches and creative in the application of techniques to different sample types.
5. Communication
Throughout the subject, you will have the opportunity to develop and utilise spoken, written and visual communication skills through the presentation of scientific research and data. Participation in group activities in practical and tutorial work will utilise and develop personal interaction and teamwork skills.
6. Critically reflect on Indigenous Australian contexts to inform professional cultural capability to work effectively with and for, Indigenous Australians within medical science, medical diagnostics and medical biotechnology.
This links to the knowledge, skills, and application component of the UTS IGA Framework where students are increasing their knowledge of Indigenous context in relation to medical science, diagnostics and biotechnology.
Professional capabilities that will be developed as part of this program are:
- Communicating and Engaging Positively with Aboriginal and Torres Strait Islander Communities.
- Free, Prior and Informed Consent; Partnering to Protect Indigenous Cultural Heritage.
- Understanding Culturally Diverse Privacy.
- Ethical Indigenous Research Practices.
- Partnership and Leadership: Inclusive Approaches for Australian Workplaces.
- Integrated understanding of the relationship between Indigenous knowledges, Indigenous research, and scientific knowledge.
Teaching and learning strategies
This subject is delivered by way of workshops, practical classes and independent learning activities. Attendance at workshops is strongly encouraged.
The content of the subject is delivered using a 'flipped' learning model, where content normally delivered in face-to-face lectures is delivered online. This is to be viewed and read by you independently prior to the relevant workshop or practical class. In workshop and practical classes, this online content is reinforced and elaborated on using a series of examples and case studies based in current research. You will be actively performing experiments and methodologies as you would in a research laboratory, making solutions from base chemicals and reagents, performing protein separating proteins by electrophoresis and chromatography, preparing samples for mass spectrometry analysis, performing data analysis and interpreting the data to reach reliable conclusions about the biology of the sample. Throughout the session, you will have 20 hours of face-to-face workshops and up to 20 hours of practical work. It is expected and necessary that you spend an equal amount of additional time completing the assigned work. During the workshops and practicals, you will have access to the subject coordinator and teaching assistants to explain and elaborate on the concepts and methodologies you will be learning. You will also learn through selected readings, video presentations, in-class collaborative activities, simulations and quizzes.
Laboratory based teaching involves hands-on experimental work. The practical sessions will explore
- sample preparation and removal of contaminants
- protein mixture fractionation
- protein separation using 1D and 2D electrophoresis.
- Mass spectrometry of proteins and peptides.
Data analysis will be performed at the individual and class level so that a statistically meaningful analysis of a larger dataset can be performed. You will work both individually and collaboratively to analyse and interpret the data.
The weekly two-hour workshop sessions are an opportunity for you to:
- learn about the fundamentals of proteomics technique enquire and raise questions relevant to proteomics
- learn how to evaluate primary scientific literature and critically assess the methods and data contained within.
- By the end of the subject, you should have a good grasp of the experimental strategies available to answer a wide variety of research problems that involve proteins.
Feedback
To ensure that you have every opportunity to understand the subject material, feedback will be constantly available to you. Teaching staff will be available in every practical class and workshop for you to ask questions and expand your knowledge of the subject. While answering questions, the teaching staff will be asking you to apply logic and knowledge for you to answer your own questions and thus gain understanding. For your written submissions, draft copies can be submitted to the teaching staff for comment and feedback prior to the due date. The teaching staff are available during face-to-face contact time and via email. In addition, forums on Canvas will be used for group discussions and general feedback.
Content (topics)
The term “proteomics” can essentially be applied to any work on proteins, whether that work involves completely cataloguing the expressed proteome of a cell, characterising the post-translational modifications of proteins at the single isoform or whole proteome level, or the characterisation of protein-protein interactions and protein complexes, to name but a brief few.
With this in mind, the objective of the practical component of this subject is to give an overview and introduction to the most common techniques used to extract, fractionate, analyse and quantitate the proteome of a cell. You will learn about protein solubilisation, fractionation strategies, protein identification by mass spectrometry, bioinformatic strategies for protein identification and quantitation methods for ascertaining expression changes. By the end of the practical component, you should have a good grasp of the experimental strategies available to answer a wide variety of research problems that involve proteins. The program of practicals outlined below is a guide to the techniques that you will learn in this subject, but the actual order of delivery may change to enhance the learning experience. Changes will be communicated to you directly in class or on Canvas with ample time for you to prepare.
As the subject is focused on teaching methodology and experimental design, each workshop will sequentially focus on a facet of proteomics methodology through examination of relevant primary literature, reviews and experience accumulated by the teaching staff.
Assessment
Assessment task 1: Designing an experimental plan
| Intent: | This assessment task contributes to the development of the following graduate attributes:
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| Objective(s): | This assessment task addresses subject learning objective(s): 1, 2 and 4 This assessment task contributes to the development of course intended learning outcome(s): 1.1, 2.1, 3.1, 4.1, 5.1 and 6.1 |
| Type: | Literature review |
| Groupwork: | Individual |
| Weight: | 30% |
| Length: | Approximately 2500 words. |
| Criteria: | The assignment will be assessed for your ability to review, analyse (disciplinary knowledge), interpret, critically evaluate (Research, inquiry and critical thinking) and appropriately communicate the findings of published literature in proteomics relevant to their chosen topic. Your report will be marked according to the following criteria:
Most importantly, ensure that you keep focused on the sample/subject/problem and write in that context, NOT generically. A marking rubric for this assessment task will be available on Canvas. |
Assessment task 2: Assessment of practical and analytical skills
| Intent: | This assessment task contributes to the development of the following graduate attributes: 1. Disciplinary knowledge |
|---|---|
| Objective(s): | This assessment task addresses subject learning objective(s): 1, 2 and 3 This assessment task contributes to the development of course intended learning outcome(s): 1.1, 2.1 and 5.1 |
| Type: | Laboratory/practical |
| Groupwork: | Individual |
| Weight: | 35% |
| Length: | This will vary between the 4 tasks |
| Criteria: | This will vary from week to week, with short answer questions and calculations to be completed |
Assessment task 3: Practical report
| Intent: | This assessment task contributes to the development of the following graduate attributes: 1. Disciplinary knowledge |
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| Objective(s): | This assessment task addresses subject learning objective(s): 1, 2, 3, 4 and 5 This assessment task contributes to the development of course intended learning outcome(s): 1.1, 2.1, 3.1, 4.1 and 5.1 |
| Type: | Report |
| Groupwork: | Individual |
| Weight: | 35% |
| Length: | 2-3000 words |
| Criteria: | The report will be assessed on your ability to produce a document of a standard suitable for publication in a designated proteomic journal as a short communication (Professional skills and their appropriate application).
In class, you will be provided with examples of best practice in drafting each of these sections. The report will be assessed on your ability to
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Minimum requirements
Students must achieve a combined grade of over 50% for all of the assessments to pass the subject.