University of Technology Sydney

91536 Proteomics

Warning: The information on this page is indicative. The subject outline for a particular session, location and mode of offering is the authoritative source of all information about the subject for that offering. Required texts, recommended texts and references in particular are likely to change. Students will be provided with a subject outline once they enrol in the subject.

Subject handbook information prior to 2020 is available in the Archives.

UTS: Science: Life Sciences
Credit points: 6 cp
Result type: Grade and marks

There are course requisites for this subject. See access conditions.

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 protein–analytical tools and information technologies to quickly and reliably identify qualitative and quantitative changes in proteins; for example, in the detection of altered protein expression associated with disease. This subject covers leading technologies for sample preparation, protein fractionations, separations and mass spectrometry for protein identification and characterisation.

In the theory component, students undertake a structured program exploring facets of experimental design and data analysis, and the best-practice sample-preparation technologies for different sample types, such as micro-organisms, plants, mammalian tissue and fluids. Written and oral assessment tasks based on the theory component 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.
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 and 2-D electrophoresis, sample preparation for mass spectrometry and basic data analysis.
4. Collect, review and critically analyse published proteomics research and methodological literature.
5. Synthesize 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.

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 the 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.

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 practice 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.

Teaching and learning strategies

This subject is delivered by way of workshops, practical classes and independent learning activities. Attendance at workshops and practical classes is compulsory.

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 24 hours of face-to-face workshops and up to 36 hours of practical work. It is expected and necessary that you spend an equal amount of additional time completing the assigned work. During the face-to-face time, 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 weekly four-hour practical sessions will explore

  • sample preparation and removal of contaminants
  • protein mixture fractionation
  • protein separation using electrophoresis and chromatography
  • 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, especially assessment tasks 1 and 4, 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: Critical Review of published literature

Intent:

This assessment task contributes to the development of the following graduate attributes:

  1. Disciplinary knowledge
  2. Research, inquiry and critical thinking
  3. Professional, ethical and social responsibility
  4. Reflection, Innovation, Creativity
  5. Communication
Type: Literature review
Groupwork: Individual
Weight: 25%
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:

  • Appropriate, recent references from the literature.
  • Logical argument based on fact and examples in the literature.
  • You MUST CRITICALLY EVALUATE the literature using knowledge you have gained throughout the subject and from other sources (Research, inquiry and critical thinking).
  • What are the advantages of the chosen methodology and are the methodologies current (Disciplinary knowledge; Research, inquiry and critical thinking; Reflection, Innovation, Creativity; Communication)?
  • What specific information will the chosen methodology provide for the specific sample/problem that other methods won’t (Disciplinary knowledge; Research, inquiry and critical thinking; Reflection, Innovation, Creativity; Professional, ethical and social responsibility, Communication)?
  • What are the disadvantages of the chosen methodology (Disciplinary knowledge; Research, inquiry and critical thinking; Reflection, Innovation, Creativity; Professional, ethical and social responsibility, Communication)?
  • Briefly mention the alternatives and the complimentary information they would provide that the chosen method won’t (Disciplinary knowledge; Research, inquiry and critical thinking; Reflection, Innovation, Creativity; Professional, ethical and social responsibility, Communication)?

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: Pre-laboratory work and calculations

Intent:

This assessment task contributes to the development of the following graduate attributes:

  1. Disciplinary knowledge
  2. Research, inquiry and critical thinking
Type: Laboratory/practical
Groupwork: Group, individually assessed
Weight: 15%
Length:

This will vary from week to week, with short answer questions and calculations to be completed.

Criteria:

The correct answers to the calculations and quiz questions. (Disciplinary knowledge; Research, inquiry and critical thinking).

Assessment task 3: Assessment of practical skills

Intent:

This assessment task contributes to the development of the following graduate attributes:

  1. Disciplinary knowledge
  2. Research, inquiry and critical thinking
  3. Communication
Type: Laboratory/practical
Groupwork: Group, individually assessed
Weight: 25%
Length:

The length of your answers is reflected in the criteria below.

Criteria:

For each of the parts:

  1. A short, one-page report describing the experiment, containing
    1. A standard graph with an R2 value of 0.9 or greater for the BCA and gel based protein assays (Disciplinary knowledge).
    2. The calculation of the total amount extracted protein from the sample for use in further experiments (Disciplinary knowledge).
    3. A brief discussion of the results and whether they are reliable and expected (Communication).
  2. Production of a correctly set and useful polyacrylamide gel, to be presented to a teaching assistant for assessment. Following electrophoresis, gel staining and destaining, the gel will be imaged and submitted via Canvas in a short, one-page report that will be assessed for correct protein loading and protein band resolution. You should also include your personal evaluation of the gel, whether it needs improvement and possible reasons for improvement based on what you have learned in the subject (Disciplinary knowledge; Research, inquiry and critical thinking; Communication).
  3. A short report displaying:
    1. MS and MS/MS spectra showing good peptide recovery from the procedure,
    2. the presence of auto-catalytic trypsin fragments indicating that the digestion has occurred successfully (Disciplinary knowledge).
    3. high quality database match with Mascot facilitated database search (Disciplinary knowledge).
    4. an interpretation of the results and their quality based on other learning tasks and workshop activities (Disciplinary knowledge; Research, inquiry and critical thinking; Communication).
  4. A short report displaying:
    1. The correct sequence of the peptide that was selected and fragmented and thus produced the MS/MS spectrum (Disciplinary knowledge).
    2. Annotation of the spectrum to show which fragment ions are evidence for the amino acid sequence (Disciplinary knowledge).
    3. Annotation of other ions that provide further evidence for the presence of specific amino acids (immonium ions) (Disciplinary knowledge).

Assessment task 4: Practical report

Intent:

This assessment task contributes to the development of the following graduate attributes:

  1. Disciplinary knowledge
  2. Research, inquiry and critical thinking
  3. Professional, ethical, and social responsibility
  4. Reflection, Innovation, Creativity
  5. Communication
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).

  • The Introduction should clearly and concisely present the experimental problem with reference to relevant current literature (Disciplinary knowledge and its appropriate application);
  • The Materials and Methods should accurately describe the technology employed (communication)
  • The Results demonstrate the ability to present proteomic data in a discipline appropriate manner (Professional skills and their appropriate application).
  • The Conclusion again will demonstrate the level of expertise gained in Disciplinary knowledge and its appropriate application, Professional skills and their appropriate application and Communication skills, and will evaluate the results in the context of the published literature.

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:

  • Produce a document in a style suitable for publication in a designated proteomic journal as a short communication (Professional skills and their appropriate application).
  • Include an Introduction that clearly and concisely present the experimental problem with reference to relevant current literature (Disciplinary knowledge);
  • Include a Materials and Methods section that accurately describe the technology employed (Disciplinary knowledge; communication)
  • Include Results that demonstrate the ability to present proteomic data in a discipline appropriate manner (Professional skills and their appropriate application).
  • Include a Conclusion that demonstrates the level of expertise gained in Disciplinary knowledge , Professional skills and their appropriate application and Communication skills, and will evaluate the results in the context of the published literature.
  • Critically evaluate the entire experiment and reflect on its quality, suggesting improvements or alternative methodologies that could improve the results and their interpretation.

Required texts

There are no essential texts.

References

Up to date references from leading proteomics, chromatography and mass spectrometry journals will be provided. Students are advised to use PubMed and consult relevent review articles prior to course commencement.