Students

MOLS8212 – Proteomics Technologies and Applications

2026 – 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
Credit points Credit points
10
Prerequisites Prerequisites
Admission to GradDipResFSE or GradCertResFSE or (BMOL6201 or BMOL6432 and Admission to GradDipBiotech or MBiotech)
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 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

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 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 technical concerns. 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. For example, if the assignment is worth 8 marks (of the entire unit) and your submission is late by 19 hours (or 23 hours 59 minutes 59 seconds), 0.4 marks (5% of 8 marks) will be deducted. If your submission is late by 24 hours (or 47 hours 59 minutes 59 seconds), 0.8 marks (10% of 8 marks) will be deducted, and so on.

  Assessments where Late Submissions will be accepted 

Practical report – Yes, Standard Late Penalty applies 

Proteomics project  – Yes, Standard Late Penalty applies 

   Assessment release dates

Practical Report – 14/9/26

Proteomics Project – 20/7/26

    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 http://connect.mq.edu.au/.

 

Assessment Tasks

Name Weighting Hurdle Due Groupwork/Individual Short Extension AI Approach
Practical Report 20% No 08/10/2026 Individual Yes Open
Proteomics Project 40% No 03/11/2026 Individual and Group No Open
Final Exam 40% No Exam period Individual No Observed

Practical Report

Assessment Type 1: Written Submission
Indicative Time on Task 2: 16 hours
Due: 08/10/2026
Weighting: 20%
Groupwork/Individual: Individual
Short extension 3: Yes
AI Approach: Open

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.


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.

Proteomics Project

Assessment Type 1: Portfolio
Indicative Time on Task 2: 31 hours
Due: 03/11/2026
Weighting: 40%
Groupwork/Individual: Individual and Group
Short extension 3: No
AI Approach: Open

You will select a recent research paper in proteomics from a curated list. You will analyse the paper and its broader research context. You will work in a group to present the paper, focusing on critical evaluation and its relevance to the unit content. You will be assessed individually on your analysis and preparation, and as a group on the presentation.


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.
  • 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.
  • Explain the chemical, biochemical and biophysical processes involved in proteomics, and demonstrate proficiency in a range of practical proteomics techniques.

Final Exam

Assessment Type 1: Examination
Indicative Time on Task 2: 31 hours
Due: Exam period
Weighting: 40%
Groupwork/Individual: Individual
Short extension 3: No
AI Approach: Observed

You will undertake a final examination during the formal examination period.


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
  • Academic Success 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.

3 An automatic short extension is available for some assessments. Apply through the Service Connect Portal.

Delivery and Resources

LECTURE, WORKSHOP and PRACTICAL TIMETABLE

 

Week 1 Classes – As shown below, our first lecture is in week 1 at 11am on Monday July 27th in 25WW A209. Our first workshop is in week 2 at 12 noon on Tuesday August 4th in 01CC 105.

 

 Lectures: Mondays 11 am – 1 pm July 27th - November 2nd, 25ww A209

 

Workshops: Tuesdays 12 noon – 1 pm August 4th - November 3rd, 01CC 105

 

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 21st - 25th. 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

Written work must be submitted through iLearn Turnitin unless specified otherwise. 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.

Unit Schedule

 

Lectures Mondays  11-1pm, starting July 27th, 25ww A209

 

Week

Date

Lecture Title

1

July 27th

Introductory Lecture - Subject Outline, assessment processes, other important information, tutorial on important concepts

2

August 3rd 

Mass spectrometry fundamentals (1)

3

August 10th

 Protein Identification from MS data (2)

4

August 17th

2D gels and 2D DIGE (3)

5

August 24th

Differential display and shotgun proteomics (4)

6

August 31st

Quantitative proteomics (I) label-free (5)

7

Sept 7th

Quantitative proteomics (II) isotope labels (6)

8

Sept 14th

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

Practical: 5 Days, 21st - 25th September (during semester break)

9

Oct 5th

No lecture, public holiday 

Practical report due Thursday October 8th

10

October 12th

Multiple reaction monitoring and proteomics validation (8)

11

October 19th

Protein-Protein Interactions (9)

12

October 26th

Post-translational modifications (I) - Glycoproteomics (10)

13

November 2nd

Post-translational modifications (II) Phosphoproteomics (11)

 

 

WORKSHOP TIMETABLE

 

Workshops: Tuesday 12 noon - 1:00 pm from August 4th, 01CC 105

             

Week

Date

Topic

1

July 28th

– no student presentations

2

August 4th 

MS Fundamentals

3

August 11th

Protein ID

4

August 18th

2D Gels and 2D DIGE

5

August 25th

Shotgun proteomics

6

September 1st  

Label Free quantitation

7

September 8th 

Quantitation with labels

8

September 15th   

Data Independent Acquisition

 

Semester Break - September 19th to October 5th      

 

9

October 6th

- No presentations - Practical report writing session

10

October 13th

Multiplexed reaction monitoring

11

October 20th

Protein interactions

12

October 27th

Glyco-Proteomics

13

November 3rd

Phospho-proteomics

 

 

Q. Why no workshop in week 1?

 

A. If we had a workshop session on that day, the students presenting their research papers would no time to prepare. If we start workshops in week two, then the first students will have a week to prepare, 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 connect.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.

Student Support

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

Academic Success

Academic Success provides resources to develop your English language proficiency, academic writing, and communication skills.

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

Student Services and Support

Macquarie University offers a range of Student Support Services including:

Student Enquiries

Got a question? Ask us via the Service Connect Portal, or contact Service Connect.

IT Help

For help with University computer systems and technology, visit https://students.mq.edu.au/support/technology/service-desk

When using the University's IT, you must adhere to the Acceptable Use of IT Resources Policy. The policy applies to all who connect to the MQ network including students.

Changes from Previous Offering

Updated lectures, updated list of papers for research presentations, and improved practical class experiments. 

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. As such, no major changes to the delivery of the unit are planned, however we will continue to strive to improve the level of support and the level of student engagement.


Unit information based on version 2026.03 of the Handbook