| Unit convenor and teaching staff |
Unit convenor and teaching staff
Paul Haynes
|
|---|---|
| Credit points |
Credit points
10
|
| Prerequisites |
Prerequisites
Admission to GradDipResFSE or GradCertResFSE or (BMOL6201 or BMOL6432 and Admission to GradDipBiotech or MBiotech)
|
| Corequisites |
Corequisites
|
| Co-badged status |
Co-badged status
|
| Unit description |
Unit description
Proteomics is the study of protein expression in living systems, considered in a functional context. This allows us to better understand how protein networks become dysfunctional, which in turn enables the manipulation of protein functions and cellular phenotypes through environmental or genetic intervention, or the use of drug treatment. This unit covers the principles and applications of proteomic techniques, and assumes basic knowledge of protein electrophoresis and mass spectrometry. Topics include: a detailed study of advanced techniques, instrumentation and protein identification software in mass spectrometry; two-dimensional differential gel electrophoresis; label-free and isotope-labelling quantitation in proteomics; application of different types of peptide- and protein-based shotgun proteomics approaches; multiplexed reaction monitoring: data independent acquisition; and characterization of protein post-translational modifications including phosphorylation and glycosylation. Students must attend a one week laboratory session during the session break. Learning in this unit enhances student understanding of global challenges identified by the United Nations Sustainable Development Goals (UNSDGs) Good Health and Well Being; Quality Education; Industry, Innovation and Infrastructure |
Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates
On successful completion of this unit, you will be able to:
Requirements to Pass this Unit
To pass this unit you must achieve a total mark equal to or greater than 50%,
Late Assessment Submission Penalty
Unless a Special Consideration request has been submitted and approved, a 5% penalty (of the total possible mark of the task) will be applied for each day a written report or presentation assessment is not submitted, up until the 7th day (including weekends). After the 7th day, a grade of ‘0’ will be awarded even if the assessment is submitted. The submission time for all uploaded assessments is 11:55 pm. A 1-hour grace period will be provided to students who experience technical concerns. For any late submission of time-sensitive tasks, such as scheduled tests/exams, performance assessments/presentations, and/or scheduled practical assessments/labs, please apply for Special Consideration. For example, if the assignment is worth 8 marks (of the entire unit) and your submission is late by 19 hours (or 23 hours 59 minutes 59 seconds), 0.4 marks (5% of 8 marks) will be deducted. If your submission is late by 24 hours (or 47 hours 59 minutes 59 seconds), 0.8 marks (10% of 8 marks) will be deducted, and so on.
Assessments where Late Submissions will be accepted
Practical report – Yes, Standard Late Penalty applies
Proteomics project – Yes, Standard Late Penalty applies
Assessment release dates
Practical Report – 14/9/26
Proteomics Project – 20/7/26
Special Consideration
The Special Consideration Policy aims to support students who have been impacted by short-term circumstances or events that are serious, unavoidable and significantly disruptive, and which may affect their performance in assessment. If you experience circumstances or events that affect your ability to complete the assessments in this unit on time, please inform the convenor and submit a Special Consideration request through http://connect.mq.edu.au/.
| Name | Weighting | Hurdle | Due | Groupwork/Individual | Short Extension | AI Approach |
|---|---|---|---|---|---|---|
| Practical Report | 20% | No | 08/10/2026 | Individual | Yes | Open |
| Proteomics Project | 40% | No | 03/11/2026 | Individual and Group | No | Open |
| Final Exam | 40% | No | Exam period | Individual | No | Observed |
Assessment Type 1: Written Submission
Indicative Time on Task 2: 16 hours
Due: 08/10/2026
Weighting: 20%
Groupwork/Individual: Individual
Short extension 3: Yes
AI Approach: Open
You must present your work in the format of a manuscript suitable for publication in a specified Proteomics Journal. This will be discussed in detail during the practical session.
Assessment Type 1: Portfolio
Indicative Time on Task 2: 31 hours
Due: 03/11/2026
Weighting: 40%
Groupwork/Individual: Individual and Group
Short extension 3: No
AI Approach: Open
You will select a recent research paper in proteomics from a curated list. You will analyse the paper and its broader research context. You will work in a group to present the paper, focusing on critical evaluation and its relevance to the unit content. You will be assessed individually on your analysis and preparation, and as a group on the presentation.
Assessment Type 1: Examination
Indicative Time on Task 2: 31 hours
Due: Exam period
Weighting: 40%
Groupwork/Individual: Individual
Short extension 3: No
AI Approach: Observed
You will undertake a final examination during the formal examination period.
1 If you need help with your assignment, please contact:
2 Indicative time-on-task is an estimate of the time required for completion of the assessment task and is subject to individual variation.
3 An automatic short extension is available for some assessments. Apply through the Service Connect Portal.
LECTURE, WORKSHOP and PRACTICAL TIMETABLE
Week 1 Classes – As shown below, our first lecture is in week 1 at 11am on Monday July 27th in 25WW A209. Our first workshop is in week 2 at 12 noon on Tuesday August 4th in 01CC 105.
Lectures: Mondays 11 am – 1 pm July 27th - November 2nd, 25ww A209
Workshops: Tuesdays 12 noon – 1 pm August 4th - November 3rd, 01CC 105
NOTE: Lectures are two hours duration and start week 1.
Practicals: Are held in a one-week block during semester break. You must be available for all of September 21st - 25th. Practical classes run about 6+ hours per day, between 9am – 5 pm. This is the equivalent of 3+ hours per week for the whole semester, we just do it all at once.
The practical course includes differential display SDS-PAGE protein electrophoresis, in-gel protein digestion, peptide mass spectrometry (nanoESI - Q Exactive orbitrap), peptide to spectrum matching using programs such as MSFragger, shotgun proteomic analysis using SDS-PAGE protein fractionation, and differential protein quantitation.
Up to date timetable information can be found found at publish.mq.edu.au
All unit information is distributed using the unit website on ilearn, accessed via ilearn.mq.edu.au
Written work must be submitted through iLearn Turnitin unless specified otherwise. Lectures and workshops will both be recorded and made available via echo 360.
We will communicate with you via your university email or through announcements on iLearn. Queries to the unit convenor can either be placed on the iLearn discussion board or sent via email from your university email address.
Lectures Mondays 11-1pm, starting July 27th, 25ww A209
|
Week |
Date |
Lecture Title |
|
1 |
July 27th |
Introductory Lecture - Subject Outline, assessment processes, other important information, tutorial on important concepts |
|
2 |
August 3rd |
Mass spectrometry fundamentals (1) |
|
3 |
August 10th |
Protein Identification from MS data (2) |
|
4 |
August 17th |
2D gels and 2D DIGE (3) |
|
5 |
August 24th |
Differential display and shotgun proteomics (4) |
|
6 |
August 31st |
Quantitative proteomics (I) label-free (5) |
|
7 |
Sept 7th |
Quantitative proteomics (II) isotope labels (6) |
|
8 |
Sept 14th |
Data dependent acquisition (DDA) and Data independent acquisition (DIA) (7) |
|
Practical: 5 Days, 21st - 25th September (during semester break) |
||
|
9 |
Oct 5th |
– No lecture, public holiday – |
|
Practical report due Thursday October 8th |
||
|
10 |
October 12th |
Multiple reaction monitoring and proteomics validation (8) |
|
11 |
October 19th |
Protein-Protein Interactions (9) |
|
12 |
October 26th |
Post-translational modifications (I) - Glycoproteomics (10) |
|
13 |
November 2nd |
Post-translational modifications (II) Phosphoproteomics (11) |
WORKSHOP TIMETABLE
Workshops: Tuesday 12 noon - 1:00 pm from August 4th, 01CC 105
|
Week |
Date |
Topic |
|
1 |
July 28th |
– no student presentations |
|
2 |
August 4th |
MS Fundamentals |
|
3 |
August 11th |
Protein ID |
|
4 |
August 18th |
2D Gels and 2D DIGE |
|
5 |
August 25th |
Shotgun proteomics |
|
6 |
September 1st |
Label Free quantitation |
|
7 |
September 8th |
Quantitation with labels |
|
8 |
September 15th |
Data Independent Acquisition |
|
|
Semester Break - September 19th to October 5th |
|
|
9 |
October 6th |
- No presentations - Practical report writing session |
|
10 |
October 13th |
Multiplexed reaction monitoring |
|
11 |
October 20th |
Protein interactions |
|
12 |
October 27th |
Glyco-Proteomics |
|
13 |
November 3rd |
Phospho-proteomics |
Q. Why no workshop in week 1?
A. If we had a workshop session on that day, the students presenting their research papers would no time to prepare. If we start workshops in week two, then the first students will have a week to prepare, which is sufficient time to allow them to do a good job.
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Updated lectures, updated list of papers for research presentations, and improved practical class experiments.
We value student feedback to be able to continually improve the way we offer our units. As such we encourage students to provide constructive feedback via student surveys, to the teaching staff directly, or via the FSE Student Experience & Feedback link in the iLearn page.
Student feedback from the previous offering of this unit was very positive overall, with students pleased with the clear communications around assessment requirements and the level of support from teaching staff. As such, no major changes to the delivery of the unit are planned, however we will continue to strive to improve the level of support and the level of student engagement.
Unit information based on version 2026.03 of the Handbook