Students

MOLS8212 – Proteomics Technologies and Applications

2023 – Session 2, In person-scheduled-weekday, North Ryde

General Information

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Unit convenor and teaching staff Unit convenor and teaching staff
Paul Haynes
paul.haynes@mq.edu.au
Credit points Credit points
10
Prerequisites Prerequisites
Admission to GradDipBiotech or GradCertLabAQMgt or GradDipLabAQMgt or MBiotech or MBioBus or MLabAQMgt or MRadiopharmSc or MSc or MScInnovationChemBiomolecularSc and (BMOL6201 or CBMS621 or BMOL6432)
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 characterisation of protein post-translational modifications including phosphorylation and glycosylation. Students must attend a compulsory one week laboratory session during the session break.

Important Academic Dates

Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates

Learning Outcomes

On successful completion of this unit, you will be able to:

  • ULO1: Process scientific data and prepare written work in formats suitable for publication in peer-reviewed scientific journals.
  • ULO2: Communicate to their peers a summary of a recent publication in a contemporary area of proteomics, and produce their own peer-review of that publication.
  • ULO3: Develop skills in critical thinking and analysis, and written and oral presentation of scientific information
  • ULO4: Extract and summarise from the scientific literature information required to develop a research plan within a relevant area of proteomics.
  • ULO5: Describe the basis of technologies used in proteomics, and exhibit sound knowledge of how to apply proteomics techniques to answer biological questions.
  • ULO6: Explain the chemical, biochemical and biophysical processes involved in proteomics, and demonstrate proficiency in a range of practical proteomics techniques.

General Assessment Information

Requirements to Pass this Unit

To pass this unit you must:

  • Attempt all assessments, and
  • 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 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, please apply for Special Consideration. 

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.

Assessment Tasks

Name Weighting Hurdle Due
Mini-Review Essay 15% No Friday September 1st
Mid-semester test 5% No week 8
Practical Report 20% No Monday October 2nd
Continuing assessment 5% No weekly
Oral Tutorial Presentation 15% No various date throughout semester
Final Exam 40% No exam period

Mini-Review Essay

Assessment Type 1: Essay
Indicative Time on Task 2: 16 hours
Due: Friday September 1st
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.

 
On successful completion you will be able to:
  • Process scientific data and prepare written work in formats suitable for publication in peer-reviewed scientific journals.
  • Develop skills in critical thinking and analysis, and written and oral presentation of scientific information
  • Extract and summarise from the scientific literature information required to develop a research plan within a relevant area of proteomics.
  • Describe the basis of technologies used in proteomics, and exhibit sound knowledge of how to apply proteomics techniques to answer biological questions.
  • Explain the chemical, biochemical and biophysical processes involved in proteomics, and demonstrate proficiency in a range of practical proteomics techniques.

Mid-semester test

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.

 
On successful completion you will be able to:
  • Develop skills in critical thinking and analysis, and written and oral presentation of scientific information
  • Describe the basis of technologies used in proteomics, and exhibit sound knowledge of how to apply proteomics techniques to answer biological questions.
  • Explain the chemical, biochemical and biophysical processes involved in proteomics, and demonstrate proficiency in a range of practical proteomics techniques.

Practical Report

Assessment Type 1: Lab report
Indicative Time on Task 2: 18 hours
Due: Monday October 2nd
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.

 
On successful completion you will be able to:
  • Process scientific data and prepare written work in formats suitable for publication in peer-reviewed scientific journals.
  • Develop skills in critical thinking and analysis, and written and oral presentation of scientific information
  • Extract and summarise from the scientific literature information required to develop a research plan within a relevant area of proteomics.
  • Describe the basis of technologies used in proteomics, and exhibit sound knowledge of how to apply proteomics techniques to answer biological questions.
  • Explain the chemical, biochemical and biophysical processes involved in proteomics, and demonstrate proficiency in a range of practical proteomics techniques.

Continuing assessment

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 day. This must be relevant to the topic that has been presented.

 
On successful completion you will be able to:
  • Develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Oral Tutorial Presentation

Assessment Type 1: Presentation
Indicative Time on Task 2: 16 hours
Due: various date throughout semester
Weighting: 15%

 

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. 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 tutorial 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.

 
On successful completion you will be able to:
  • Communicate to their peers a summary of a recent publication in a contemporary area of proteomics, and produce their own peer-review of that publication.
  • Develop skills in critical thinking and analysis, and written and oral presentation of scientific information
  • Extract and summarise from the scientific literature information required to develop a research plan within a relevant area of proteomics.
  • Describe the basis of technologies used in proteomics, and exhibit sound knowledge of how to apply proteomics techniques to answer biological questions.

Final Exam

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 MOLS8212. Questions are a mix of long and short answer questions

 
On successful completion you will be able to:
  • Develop skills in critical thinking and analysis, and written and oral presentation of scientific information
  • Describe the basis of technologies used in proteomics, and exhibit sound knowledge of how to apply proteomics techniques to answer biological questions.
  • Explain the chemical, biochemical and biophysical processes involved in proteomics, and demonstrate proficiency in a range of practical proteomics techniques.

1 If you need help with your assignment, please contact:

  • the academic teaching staff in your unit for guidance in understanding or completing this type of assessment
  • the Writing Centre for academic skills support.

2 Indicative time-on-task is an estimate of the time required for completion of the assessment task and is subject to individual variation

Delivery and Resources

LECTURE, Workshop and PRACTICAL TIMETABLE

Lectures: Mondays 10:00am – 12 noon July 24th - October 30th, 01CC 215

Tutorial workshops: Wednesdays 3:00 – 4:00 pm July 26th - November 1st, 01CC 116

 

NOTE: Lectures are two hours duration and start week 1, and will include the first scientific content lecture (Monday 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 (Wednesday July 26th).

Practicals: Are held in a one-week block during semester break. You must be available for all of September 11th- 15th. 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 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 timetables.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 tutorial workshops will both be recorded and made available via echo 360.

For 2023, we will have no classes in week two (July 31st) and week ten of semester (October 9th). We will also need to have pre-recorded lectures in week three (August 7th) and week nine (October 2nd).

 

Delivery

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.

 

Unit Schedule

Lectures Mondays  10-12pm, starting July 24th, 01CC 215

 

Week

Date

Lecture Title

1

Monday July 24th

Mass spectrometry fundamentals (1)

1

Wednesday

July 26th

Introductory Lecture - Subject Outline, assessment processes, and other important information (in tutorial timeslot)

2

July 31st

No lecture or tutorial, PH absent.

3

August 7th

 Protein Identification from MS data (2) – recorded lecture, no in-person attendance

4

August 14th

2D gels and 2D DIGE (3)

5

August 21st

Differential display and shotgun proteomics (4)

6

August 28th

Quantitative proteomics (I) label-free (5)

7

Sept 4th

Quantitative proteomics (II) isotope labels (6)

Practical: 5 Days, 11th- 15th September (during semester break)

8

Sept 25th

Data dependent acquisition (DDA) and Data independent acquisition (DIA) (7)

Practical report due Monday October 2nd

9

October 2nd

– public holiday – recorded lecture, no in person attendance.

 Multiple reaction monitoring and proteomics validation (8)

10

October 9th

No Lecture – PH on field trip

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)

 

MOLS8212 Proteomics Technologies and Applications

 

Workshop TIMETABLE

 

Workshops: Wednesdays 3:00 - 4:00 pm from August 5th, 01CC 116

           

Week

Date

1

[note: July 26th is used for an introductory lecture]

2

August 2nd - No workshop.

3

August 9th - MS Fundamentals

4

August 16th - Protein ID

5

August 23rd - 2D Gels and 2D DIGE

6

August 30rd - Shotgun proteomics

7

September 6th - Quantitation with labels

 

 

Semester Break - September 11th to September 24th                            

8

September 27th – Label Free quantitation

9

October 4th - Data Independent Acquisition

10

October 11th – No workshop, PH away on field trip.

11

October 18th – Multiplexed reaction monitoring

12

October 25th  - Protein interactions

13

November 1st - Glycoproteomics  + Phosphoproteomics

 

 

 

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 their presentations, which is sufficient time to allow them to do a good job.

 

 

Policies and Procedures

Macquarie University policies and procedures are accessible from Policy Central (https://policies.mq.edu.au). Students should be aware of the following policies in particular with regard to Learning and Teaching:

Students seeking more policy resources can visit Student Policies (https://students.mq.edu.au/support/study/policies). It is your one-stop-shop for the key policies you need to know about throughout your undergraduate student journey.

To find other policies relating to Teaching and Learning, visit Policy Central (https://policies.mq.edu.au) and use the search tool.

Student Code of Conduct

Macquarie University students have a responsibility to be familiar with the Student Code of Conduct: https://students.mq.edu.au/admin/other-resources/student-conduct

Results

Results published on platform other than eStudent, (eg. iLearn, Coursera etc.) or released directly by your Unit Convenor, are not confirmed as they are subject to final approval by the University. Once approved, final results will be sent to your student email address and will be made available in eStudent. For more information visit ask.mq.edu.au or if you are a Global MBA student contact globalmba.support@mq.edu.au

Academic Integrity

At Macquarie, we believe academic integrity – honesty, respect, trust, responsibility, fairness and courage – is at the core of learning, teaching and research. We recognise that meeting the expectations required to complete your assessments can be challenging. So, we offer you a range of resources and services to help you reach your potential, including free online writing and maths support, academic skills development and wellbeing consultations.

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Macquarie University provides a range of support services for students. For details, visit http://students.mq.edu.au/support/

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The Library provides online and face to face support to help you find and use relevant information resources. 

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Changes from Previous Offering

Updated lectures, updated list of papers for research presentations.

Changes since First Published

Date Description
19/07/2023 Updated to correct room number for workshop.

Unit information based on version 2023.01R of the Handbook