Late Assessment Submission Penalty

 

From 1 July 2022, Students enrolled in Session based units with written assessments will have the following university standard late penalty applied. Please see https://students.mq.edu.au/study/assessment-exams/assessments for more information.

Unless a Special Consideration request has been submitted and approved, a 5% penalty (of the total possible mark) will be applied each day a written 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. Submission time for all written assessments is set at 11:55 pm. A 1-hour grace period is provided to students who experience a technical concern.  For any late submission of time-sensitive tasks, such as scheduled tests/exams, performance assessments/presentations, and/or scheduled practical assessments/labs, students need to submit an application for Special Consideration. 

In this unit, late submissions will be accepted for the essay and practical report, both of which are written tasks with a specified due date.

 

 

LECTURE, TUTORIAL and PRACTICAL TIMETABLE

 

Lectures: Thursdays 12 noon - 2:00 pm July 28^th - November 3^rd, 4 Western Rd 220

 

Tutorial workshops: Fridays 11:00 am – 12 noon am July 29^th - November 4^th, 14SCO 263

 

NOTE: Lectures start week 1, and an introductory lecture explaining all aspects of the course 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 12^th- 16^th. 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

 

 

 

 

 

 

 

Lectures Thursdays 12-2pm, starting July 28^th, 4 Western Rd 220

 

Week	Date	Lecture Title
1	THURSDAY July 28th	Mass spectrometry fundamentals (1)
1	FRIDAY July 29th	Introductory Lecture - Subject Outline, assessment processes, and other important information (in tutorial timeslot)
2	August 4th	Protein Identification from MS data (2)
3	August 11th	2D gels and 2D DIGE (3)
4	August 18th	Differential display and shotgun proteomics (4)
5	August 25th	Quantitative proteomics (I) label-free (5)
6	Sept 1st	Quantitative proteomics (II) isotope labels (6)
7	Sept 8th	Data dependent acquisition (DDA) and Data independent acquisition (DIA) (7)
Practical: 5 Days, 12th- 16th September (during semester break)
8	Sept 29th	Multiple reaction monitoring and proteomics validation (8)
Practical report due Monday October 3rd
9	October 6th	Protein-Protein Interactions (9)
10	October 13th	Post-translational modifications (I) Glycoproteomics (10)
11	October 20th	Post-translational modifications (II) Phosphoproteomics (11)
12	October 27th	Revision (12)
13	November 3rd	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.

MOLS8212 Proteomics Technologies and Applications

 

TUTORIAL TIMETABLE

 

Tutorials: Fridays 11am-12 from August 1^st, 14SCO 263

           

Week	Date
1	[note: July 29th is used for an introductory lecture]
2	August 5th - MS Fundamentals
3	August 12th - Protein ID
4	August 19th - 2D Gels and 2D DIGE
5	August 26th - Shotgun proteomics
6	September 2nd - Label Free quantitation
7	September 9th - Quantitation with labels
	Semester Break - September 10th to September 25th
8	September 30th – Data Independent Acquisition
9	October 7th - Multiplexed reaction monitoring
10	October 14th - Protein interactions
11	October 21st - Glycoproteomics
12	October 28th - Phosphoproteomics
13	November 4th - spare

 

 

Q. Why is July 29th used for an introductory 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.

 

 

 

 

MOLS8212 Proteomics Technologies and Applications

ASSESSMENT PROCESS 2022

 

Mini-Review Essay (Due Friday September 2^nd) - 15%

 

Topic for 2022: Compare and contrast the way in which proteomics studies are performed in current literature as opposed to those performed ten years ago. 

 

• 1200-1500 word mini-review article suitable for publication (not including titles, affiliations, abstract, keywords, acknowledgements, 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. Hint: go to Pubmed and search for “Journal of Proteomics AND review”.
• You can choose to focus on a particular biological subject area if you wish, but you must make that clear to the reader.

 

Group Oral Tutorial Presentation – Various Dates -   15%

 

• You will work in groups of two, so identify a partner as soon as possible.
• Choose one publication from the Tutorial Papers List (on a first-come first-served basis), which is found on a wiki on the iLearn site.
• The papers are to be presented on the date indicated, because they are sorted by subject material. There is a small number of general interest papers at the end of the list which can be presented on any date you wish to choose.
• A maximum of two group presentations will be scheduled for each week. If you put your name down on a particular date as the third group, you will miss out on presenting, so you will have wasted your time.
• Both students must take part in presenting, and share the workload.
• An essential part of this task is organising yourselves so that everyone in the class has a time scheduled to present their work. A wiki will be set up in iLearn, and you will be able to put your name down. The papers are grouped by subject so that they follow the weekly lecture content fairly closely, to help reinforce your learning. Hence, a paper on a specific topic will be listed on a given date and can only be presented on that date.
• The exception to this is the general interest papers which can be presented on any date you wish to choose. If you choose to present one of the general interest papers, it is your job to copy and paste that information into the correct date on the wiki so that everyone knows what is going on.
• It is important to be proactive about this scheduling task, because the unit convenor will not be involved. If there are three or four group names down to present on one week, you need to talk among yourselves and fix the problem. Please be aware that we frequently have issues with students putting their name down and then withdrawing from the unit. That means timeslots go by unused and then there is not enough time for other students to present. Again, it is the responsibility of all students involved to make sure that we get two presentations each week.
• Present your critique of the topic as a short Powerpoint seminar. Aim for 10 min talking (12 minutes absolute max), and there will be time for questions And discussions. We may adjust that schedule depending on class numbers.
• Summarise the paper. Present it in a short form so that other students in the class can understand what was done, and how, and why.
• You are not required to present every figure and table from the paper, you need to summarise and present what is important to get the point across.
• 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.
• Participation in all other group’s topic presentations contributes to your final mark - if you turn up and ask questions, you will get a better mark. Since this constitutes a continuing assessment component, marks will not be finalised and released until the last presentation has been completed at the end of the semester.
• The research tutorial presentation can be presented live, or it can also be presented as a video presentation uploaded in advance to youtube. Pre-recorded videos 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. Tutorial presentations will be recorded and made available via iLearn.

 

Continuing assessment: Weekly Speaker Questions - 5%

 

• You will be given a few minutes at the end of each lecture so that you can write down and submit a question concerning the lecture of the day. This must be relevant to the topic that has been presented.

 

Mid-semester test – week 8 - 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, date to be confirmed.

 

Practical Report (Due Monday October 3^rd) - 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.

  

Final Exam (2.5 hrs, date and time to be advised) - 40%

 

• 2.5hr exam covering all practical and theoretical components of MOLS8212
• Questions are a mix of long and short answer questions

 

 

 

 

 

Late Assessment Submission Penalty

 

From 1 July 2022, Students enrolled in Session based units with written assessments will have the following university standard late penalty applied. Please see https://students.mq.edu.au/study/assessment-exams/assessments for more information.

Unless a Special Consideration request has been submitted and approved, a 5% penalty (of the total possible mark) will be applied each day a written 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. Submission time for all written assessments is set at 11:55 pm. A 1-hour grace period is provided to students who experience a technical concern.  For any late submission of time-sensitive tasks, such as scheduled tests/exams, performance assessments/presentations, and/or scheduled practical assessments/labs, students need to submit an application for Special Consideration. 

In this unit, late submissions will be accepted for the essay and practical report, both of which are written tasks with a specified due date.

 

 

 

 

 

TUTORIAL TOPICS

EVALUATION CRITERIA

 

Your tutorial presentation (approximately 10-12min presentation plus question time, depending on student numbers) will be assessed using the following criteria.

 

1. Content – is your presentation accurate and easy to understand, and evidence of sound knowledge of the overall subject area
2. Evidence of comprehension of techniques used
3. Evidence of literature research beyond the set text
4. Fluency and presentation, including use of visual, and ability to maintain group attention
5. Inclusion of key advances in the area
6. Demonstration of critical scientific thinking
7. Assessment of any relevant ethical and social issues
8. Summing up with a peer-review recommendation: do you think this work should have been published or not? Why?
9. Handling of questions
10. Participation in other student's tutorial presentations i.e. pay attention and ask intelligent questions

 

 

 

 

  Other important items

 

• We do not work from a textbook, instead we focus on current scientific literature.

• Additional reading material is also included at the end of most lectures. It is your job to look it up.

• The practical class is 5 days long and runs during semester break, so make plans now to be available for a week long practical class during that time.

• Technologies used and required. Lecture notes will be made available on the unit website in iLearn. Notes will be made available a few days in advance of the lecture whenever possible, and it is your responsibility to bring your own copy to lectures.

• Technologies used and required. All of the important information during semester will be communicated to you via the unit website on iLearn. It is your responsibility to check it regularly for announcements and other information.

• Technologies used and required. Students will need to have access to a computer and printer, and be able to use Word, Excel, Powerpoint, and a reference manager program such as EndNote.

• What is changed? The unit is updated every year with revised lecture content and numerous new tutorial research papers.

• What is changed? The unit has been renamed to Proteomics Technologies and Applications, to better capture what the unit is intending to convey.

• What is changed? The research tutorial presentation will 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.
• For 2022, revised and refreshed lecture content based on feedback from the previous year, and updated tutorial paper list. The revised lecture content and numerous new tutorial research papers reflect the rapidly changing state of the field.