Unit convenor and teaching staff |
Unit convenor and teaching staff
Convenor, Lecturer, Tutor
Paul Haynes
Demonstrator, Tutor
Karlie Neilson
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Credit points |
Credit points
10
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Prerequisites |
Prerequisites
Admission to GradDipResFSE or GradCertResFSE or (BMOL6201 or BMOL6432 and Admission to GradDipBiotech or MBiotech)
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Corequisites |
Corequisites
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Co-badged status |
Co-badged status
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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:
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 a technical concern.
Assessments where Late Submissions will be accepted
This applies to all submitted assessments.
Special Consideration
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.
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 ask.mq.edu.au.
Name | Weighting | Hurdle | Due |
---|---|---|---|
Final Exam | 40% | No | exam period |
Practical Report | 20% | No | Tuesday October 13th |
Proteomics Project | 40% | No | week 13 |
Assessment Type 1: Examination
Indicative Time on Task 2: 31 hours
Due: exam period
Weighting: 40%
Written exam covering all practical and theoretical components of the unit curriculum. Includes a mix of long and short answer questions.
Assessment Type 1: Lab report
Indicative Time on Task 2: 16 hours
Due: Tuesday October 13th
Weighting: 20%
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: Project
Indicative Time on Task 2: 31 hours
Due: week 13
Weighting: 40%
Each student will choose a recent relevant paper in the field of Proteomics, from a broader list sorted by subject matter. The project includes researching and analyzing the paper and the relevant subject matter and delivering a short talk to the class explaining the paper, and how it fits in with the literature context and the unit curriculum. Initial preparation and research work examining the selected paper will be assessed individually, while the oral presentation will be delivered and assessed as a group project.
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
LECTURE, WORKSHOP and PRACTICAL TIMETABLE
Week 1 Classes – As shown below, our first lecture is in week 1 at 1pm on Wednesday July 30th in 25WW A207. There is no workshop scheduled in week 1, so our first workshop is in week 2 at 3pm on Thursday August 7th in 21ww 2.300.
Lectures: Wednesdays 1:00 pm – 3:00 pm July 30th - November 5th, 25ww A207
Workshops: Thursdays 3:00 pm – 4:00 pm July 31st - November 6th, 21ww 2.300
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 22nd- 26th. 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
All written work must be submitted through iLearn Turnitin. 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 - Wednesdays 1-3pm, starting July 30th, 25ww A207
Week |
Date |
Lecture Title and (number) |
1 |
Wednesday July 30th |
Introductory Lecture - Subject Outline, assessment processes, and other important information |
2 |
August 6th |
Mass spectrometry fundamentals (1) |
3 |
August 13th |
Protein Identification from MS data (2) |
4 |
August 20th |
2D gels, 2D DIGE and experimental design (3) |
5 |
August 27th |
Differential display and shotgun proteomics (4) |
6 |
Sept 3rd |
Quantitative proteomics (I) label-free (5) |
7 |
Sept 10th |
Quantitative proteomics (II) isotope labels (6) |
8 |
Sept 17th |
Data dependent acquisition (DDA) and Data independent acquisition (DIA) (7) |
Practical: 5 Days, 22nd- 25th September (during semester break) |
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9 |
Oct 8th |
Multiple reaction monitoring and proteomics validation (8) |
Practical report due Monday October 13th |
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10 |
October 15th |
Protein-Protein Interactions (9) |
11 |
October 22nd |
Post-translational modifications (I) Glycoproteomics (10) |
12 |
October 29th |
Post-translational modifications (II) Phosphoproteomics (11) |
13 |
November 5th |
Revision |
WORKSHOP TIMETABLE
Workshops: Thursdays 3:00 - 4:00 pm from August 7th, 21ww 2.300
Week |
Date |
|
1 |
Thursday July 31sth – no workshop |
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2 |
August 7th |
MS Fundamentals |
3 |
August 14th |
Protein ID |
4 |
August 21st |
2D Gels and 2D DIGE |
5 |
August 28th |
Shotgun proteomics |
6 |
September 4th |
Label Free quantitation |
7 |
September 11th |
Quantitation with labels |
8 |
September 18th |
Data Independent Acquisition |
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Semester Break - September 20th to October 6th |
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9 |
October 9th |
Multiplexed reaction monitoring |
10 |
October 16th |
Protein interactions |
11 |
October 23rd |
Glyco-proteomics |
12 |
October 30th |
Phospho-proteomics |
13 |
November 6th |
Spare |
Q. Why no workshop in week 1?
A. If we had a workshop session on that day, the students presenting their research papers would have no time to prepare. If we start workshops in week two, then the first students will have sufficient time to prepare, which will allow them to do a good job.
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Updated lectures, updated list of papers for research presentations, and redesigned practical class experiments.
Updated and revised assessment tasks and descriptions to fit with the new three assessment policy.
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.
Unit information based on version 2025.07 of the Handbook