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
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:
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 |
---|---|---|---|
Oral Workshop Presentation | 15% | No | Various dates throughout the semester |
Continuing assessment | 5% | No | weekly |
Final Exam | 40% | No | Exam period |
Practical Report | 20% | No | 8th October |
Mid-semester test | 5% | No | week 9 |
Mini-Review Essay | 15% | No | Friday 6th September |
Assessment Type 1: Presentation
Indicative Time on Task 2: 16 hours
Due: Various dates throughout the semester
Weighting: 15%
Choose one publication from the Workshop Papers List (on a first-come first-served basis), which is found on a wiki 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 research workshop presentation will now be accepted as a video presentation uploaded in advance to youtube. It must include figures, graphics, text (and some footage of the presenter). You can either record straight to video camera, or use software such as iMovie or Windows Movie Maker.
Assessment Type 1: Reflective Writing
Indicative Time on Task 2: 3 hours
Due: weekly
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: 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.
Assessment Type 1: Lab report
Indicative Time on Task 2: 18 hours
Due: 8th October
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: Quiz/Test
Indicative Time on Task 2: 3 hours
Due: week 9
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: Essay
Indicative Time on Task 2: 16 hours
Due: Friday 6th September
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.
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
Lectures: Wednesdays 1pm – 3pm July 24th - October 30th, 01CC 203
Workshops: Fridays 12 noon – 1pm July 26th - November 1st, 01CC 106
NOTE: Lectures are two hours duration and start week 1, and will include the first scientific content lecture (Wednesday July 24th) followed by the introductory lecture explaining all aspects of the course – which is only one hour long – followed in the first workshop timeslot (Friday July 26th).
Practicals: Are held in a one-week block during semester break. You must be available for all of September 16th- 20th. 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 MaxQuant and MSFragger, shotgun proteomic analysis using SDS-PAGE protein fractionation, and differential protein quantitation.
Up to date timetable information is 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.
For 2024, we will have no in-person classes in week 5 (commencing august 19th) and week 10 (commencing October 7th) of semester. Please read the lecture and workshop schedule very carefully.
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.
COVID Information
For the latest information on the University’s response to COVID-19, please refer to the Coronavirus infection page on the Macquarie website: https://www.mq.edu.au/about/coronavirus-faqs. Remember to check this page regularly in case the information and requirements change during semester. If there are any changes to this unit in relation to COVID, these will be communicated via iLearn.
Lectures Wednesdays 1-3pm, starting July 24th, 01CC 203
Week |
Date |
Lecture Title |
1 |
Wednesday July 24th |
Mass spectrometry fundamentals (1) |
1 |
Friday July 26th |
Introductory Lecture - Subject Outline, assessment processes, and other important information (in workshop timeslot) |
2 |
July 31st |
Protein Identification from MS data (2) |
3 |
August 7th |
2D gels and 2D DIGE (3) |
4 |
August 14th |
Differential display and shotgun proteomics (4) |
5 |
August 21st |
No lecture, PH absent |
6 |
August 28th |
Quantitative proteomics (I) label-free (5) |
7 |
Sept 4th |
Quantitative proteomics (II) isotope labels (6) |
8 |
Sept 11th |
Data dependent acquisition (DDA) and Data independent acquisition (DIA) (7) |
Practical: 5 Days, 16th- 20th September (during semester break) |
||
9 |
Oct 2nd |
Multiple reaction monitoring and proteomics validation (8) |
Practical report due Tues October 8th |
||
10 |
October 9th |
– No lecture, PH absent – |
11 |
October 16th |
Protein-Protein Interactions (9) |
12 |
October 23rd |
Post-translational modifications (I) Glycoproteomics (10) |
13 |
October 30th |
Post-translational modifications (II) Phosphoproteomics (11) |
MOLS7212 Proteomics Technologies and Applications
WORKSHOP TIMETABLE
Workshops: Fridays 12 noon - 1:00 pm from August 5th, 01CC 106
Week |
Date |
|
1 |
July 26th – no workshop, but we have an … |
… introductory lecture |
2 |
August 2nd |
MS Fundamentals |
3 |
August 9th |
Protein ID |
4 |
August 16th |
2D Gels and 2D DIGE |
5 |
August 23rd |
No workshop, PH absent |
6 |
August 30th |
Shotgun proteomics |
7 |
September 6th |
Label Free quantitation |
8 |
September 13th |
Quantitation with labels |
|
Semester Break - September 14th to September 29th |
|
9 |
October 4th |
Data Independent Acquisition |
10 |
October 11th |
No workshop, PH absent |
11 |
October 18th |
Multiplexed reaction monitoring |
12 |
October 25th |
Protein interactions |
13 |
November 1st |
Glyco- and Phospho-proteomics |
Q. Why is July 26th used for an introductory lecture?
A. If we had a workshop session on that day, the students presenting their research papers would have less than a week to prepare. If we start workshops 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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Updated lectures, updated list of papers for research presentations, and redesigned practical class experiments.
Unit information based on version 2024.03 of the Handbook