Session 2 Learning and Teaching Update
The decision has been made to conduct study online for the remainder of Session 2 for all units WITHOUT mandatory on-campus learning activities. Exams for Session 2 will also be online where possible to do so.
This is due to the extension of the lockdown orders and to provide certainty around arrangements for the remainder of Session 2. We hope to return to campus beyond Session 2 as soon as it is safe and appropriate to do so.
Some classes/teaching activities cannot be moved online and must be taught on campus. You should already know if you are in one of these classes/teaching activities and your unit convenor will provide you with more information via iLearn. If you want to confirm, see the list of units with mandatory on-campus classes/teaching activities.
Visit the MQ COVID-19 information page for more detail.
Unit convenor and teaching staff |
Unit convenor and teaching staff
Paul Haynes
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Credit points |
Credit points
10
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Prerequisites |
Prerequisites
Admission to MRes
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Corequisites |
Corequisites
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Co-badged status |
Co-badged status
Co-taught with Mols8212.
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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 characterisation of protein post-translational modifications including phosphorylation and glycosylation. Students must attend a compulsory one week laboratory session during the semester break. |
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:
Name | Weighting | Hurdle | Due |
---|---|---|---|
Mini-Review Essay | 15% | No | Friday September 3rd 9am |
Mid-semester test | 5% | No | week 8 |
Practical Report | 20% | No | Monday October 4th 9am |
Continuing assessment | 5% | No | ongoing |
Oral Tutorial Presentation | 15% | No | Various dates available |
Final Exam | 40% | No | Exam Period |
Assessment Type 1: Essay
Indicative Time on Task 2: 16 hours
Due: Friday September 3rd 9am
Weighting: 15%
Topic: Compare and contrast the way in which proteomics studies are performed in current literature as opposed to those performed ten years ago. 2000 word mini-review article suitable for publication (not including references, diagrams, tables or figures, all of which are encouraged) Must conform to the Instructions for Authors for a review article submitted to “Journal of Proteomics”. Look up the Journal of Proteomics instructions and follow them. Make sure you read some review articles in the journal before you start writing, because that will give you a good template to work from.
Assessment Type 1: Quiz/Test
Indicative Time on Task 2: 3 hours
Due: week 8
Weighting: 5%
This will typically be a short quiz aimed at helping students assess their areas of strength and weakness prior to the final exam. It will be held after the midsemester break.
Assessment Type 1: Lab report
Indicative Time on Task 2: 18 hours
Due: Monday October 4th 9am
Weighting: 20%
You must present your work in the format of a manuscript suitable for publication in Journal of Proteomics. This will be discussed in detail during the practical session.
Assessment Type 1: Reflective Writing
Indicative Time on Task 2: 3 hours
Due: ongoing
Weighting: 5%
You will be given 5 minutes at the end of each lecture in which you are required to write down and submit a question concerning the lecture for the the day. This must be relevant to the topic that has been presented.
Assessment Type 1: Presentation
Indicative Time on Task 2: 16 hours
Due: Various dates available
Weighting: 15%
Choose one publication from a Tutorial Papers List (on a first-come first-served basis), which is found on the iLearn site. Present your critique of the topic as a short Powerpoint seminar. Aim for 10-12 min talking (15 minutes max), and there will be time for questions. We may adjust that schedule depending on class numbers. Participation in all other group’s topics contributes to your final mark. Perform your own peer-review of your chosen paper - tell us whether you think this paper should have been published and why. Look up other relevant literature so you can discuss your chosen paper in context rather than in isolation. The presentationcan be submitted as a video presentation uploaded in advance to youtube. It must include figures, graphics, text (and some footage of the presenter).
Assessment Type 1: Examination
Indicative Time on Task 2: 22 hours
Due: Exam Period
Weighting: 40%
2.5hr exam covering all practical and theoretical components of MOLS7212 Questions are a mix of long and short answer questions.
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
MOLS7212 Proteomics Technologies and Applications
LECTURE, TUTORIAL and PRACTICAL TIMETABLE
Lectures: Thursdays 10:00 am - 12:00 pm July 29th - November 4th, either 9WW 102 or online
Tutorials/workshops: Fridays 10:00 am - 11:00 am July 30th - November 5th, either 3IR G240 or online
NOTE: the first scientific content lecture will be delivered in the first tutorial timeslot.
Practicals: Are held in a one-week block during semester break. You must be available for all of September 13th- 17th. 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. Attendance is compulsory - if you are not able to attend the practical class all week, for any reason, please do not enrol in this unit.
The practical course includes differential display 2D gel electrophoresis, in-gel protein digestion, peptide spectrometry (MALDI-TOF/TOF and nanoESI-Linear ion trap), protein identification using Mascot and XTandem, shotgun proteomic analysis using SDS-PAGE protein fractionation, and label-free protein quantitation using normalized spectral abundance factors.
Up to date timetable information is found at timetables.mq.edu.au
All unit information is distributed using the unit website on ilearn, accessed via ilearn.mq.edu.au
MOLS7212 Proteomics Technologies and Applications
ASSESSMENT PROCESS 2021
Mini-Review Essay (Due 9am Friday September 3rd) - 15%
Topic for 2021: Compare and contrast the way in which proteomics studies are performed in current literature as opposed to those performed ten years ago.
Group Oral Tutorial Presentation – Various Dates 15%
Continuing assessment: Weekly Speaker Questions - 5%
Note that in the event of a Coronavirus global pandemic:
Mid-semester test – week 8 - 5%
Practical Report (Due Monday October 4th) - 20%
Final Exam (2.5 hrs, date and time to be advised) - 40%
Lectures Thursdays 10-12pm, starting July 29th, 9WW102 or online
Week |
Date |
Lecture Title |
1 |
THURSDAY July 29th |
Subject Outline, Introduction and Assessment Process, and General Introduction (1) |
1 |
FRIDAY July 30th |
Mass spectrometry fundamentals (2) (in tutorial timeslot) |
2 |
August 5th |
Protein Identification from MS data (3) |
3 |
August 12th |
2D gels and 2D DIGE (4) |
4 |
August 19th |
Differential display and shotgun proteomics (5) |
5 |
August 26th |
Quantitative proteomics (I) label-free (6) |
6 |
Sept 2nd |
Quantitative proteomics (II) isotope labels (7) |
7 |
Sept 9th |
Data dependent acquisition (DDA) and Data independent acquisition (DIA) (8) |
Practical: 5 Days, 13th- 17th September (during semester break) |
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8 |
Sept 30th |
Multiple reaction monitoring and proteomics validation (9) |
9 |
October 7th |
Protein-Protein Interactions (10) [Public Holiday] |
Practical report due 9am Monday October 4th
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10 |
October 14th |
Post-translational modifications (I) Glycoproteomics (11) |
11 |
October 21st |
Post-translational modifications (II) Phosphoproteomics (12) |
12 |
October 28th |
Revision |
13 |
November 4th |
Spare |
All written work must be submitted through iLearn Turnitin. In addition, hardcopies may be required, to be confirmed. Lectures and tutorials will both be recorded and made available via echo 360.
MOLS7212 Proteomics Technologies and Applications
TUTORIAL TIMETABLE
Tutorials: Fridays 10-11am from August 2nd, 3IR G240 or online
Week |
Date |
1 |
[note: July 30th is used for a lecture] |
2 |
August 6th - MS Fundamentals |
3 |
August 13th - Protein ID |
4 |
August 20th - 2D Gels and 2D DIGE |
5 |
August 27th - Shotgun proteomics |
6 |
September 3rd - Label Free quantitation |
7 |
September 10th - Quantitation with labels |
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Semester Break - September 11th to September 26th |
8 |
October 1st – Data Independent Acquisition |
9 |
October 8th - Multiplexed reaction monitoring |
10 |
October 15th - Protein interactions |
11 |
October 22nd - Glycoproteomics |
12 |
October 29th - Phosphoproteomics |
13 |
November 5th - spare |
Q. Why is July 30 used for a lecture?
A. If we had a tutorial session on that day, the students presenting their research papers would have less than a week to prepare. If we start tutorials in week two, then the first students will have two weeks to prepare, which is sufficient time to allow them to do a good job.
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Unit information based on version 2021.03 of the Handbook