Students

MOLS8212 – Proteomics Technologies and Applications

2025 – Session 2, In person-scheduled-weekday, North Ryde

General Information

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Unit convenor and teaching staff Unit convenor and teaching staff Convenor, Lecturer, Tutor
Paul Haynes
Demonstrator, Tutor
Karlie Neilson
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:

  • 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.

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.

Assessment Tasks

Name Weighting Hurdle Due
Final Exam 40% No exam period
Practical Report 20% No Tuesday October 13th
Proteomics Project 40% No week 13

Final Exam

Assessment Type 1: Examination
Indicative Time on Task 2: 31 hours
Due: exam period
Weighting: 40%

 

Written exam covering all practical and theoretical components of the unit curriculum. Includes 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.

Practical Report

Assessment Type 1: Lab report
Indicative Time on Task 2: 16 hours
Due: Tuesday October 13th
Weighting: 20%

 

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: Project
Indicative Time on Task 2: 31 hours
Due: week 13
Weighting: 40%

 

Each student will choose a recent relevant paper in the field of Proteomics, from a broader list sorted by subject matter. The project includes researching and analyzing the paper and the relevant subject matter and delivering a short talk to the class explaining the paper, and how it fits in with the literature context and the unit curriculum. Initial preparation and research work examining the selected paper will be assessed individually, while the oral presentation will be delivered and assessed as a group project.

 


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.

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

Week 1 Classes – As shown below, our first lecture is in week 1 at 1pm on Wednesday July 30th in 25WW A207. There is no workshop scheduled in week 1, so our first workshop is in week 2 at 3pm on Thursday August 7th in 21ww 2.300.

 

Lectures: Wednesdays 1:00 pm – 3:00 pm July 30th - November 5th, 25ww A207

Workshops: Thursdays 3:00 pm – 4:00 pm July 31st - November 6th, 21ww 2.300

 

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 22nd- 26th. 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

 All written work must be submitted through iLearn Turnitin. 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 - Wednesdays  1-3pm, starting July 30th, 25ww A207

Week

Date

Lecture Title and (number)

1

Wednesday July 30th

Introductory Lecture - Subject Outline, assessment processes, and other important information

2

August 6th

Mass spectrometry fundamentals (1)

3

August 13th

 Protein Identification from MS data (2)

4

August 20th

2D gels, 2D DIGE and experimental design (3)

5

August 27th

Differential display and shotgun proteomics (4)

6

Sept 3rd

Quantitative proteomics (I) label-free (5)

7

Sept 10th

Quantitative proteomics (II) isotope labels (6)

8

Sept 17th

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

Practical: 5 Days, 22nd- 25th September (during semester break)

9

Oct 8th

Multiple reaction monitoring and proteomics validation (8)

Practical report due Monday October 13th  

10

October 15th

Protein-Protein Interactions (9)

11

October 22nd

Post-translational modifications (I) Glycoproteomics (10)

12

October 29th

Post-translational modifications (II) Phosphoproteomics (11)

13

November 5th

Revision

 

 

WORKSHOP TIMETABLE

Workshops: Thursdays 3:00 - 4:00 pm from August 7th, 21ww 2.300

Week

Date

 

1

Thursday July 31sth – no workshop

 

2

August 7th

MS Fundamentals

3

August 14th

Protein ID

4

August 21st

2D Gels and 2D DIGE

5

August 28th

Shotgun proteomics

6

September 4th  

Label Free quantitation

7

September 11th   

Quantitation with labels

8

September 18th   

Data Independent Acquisition

 

Semester Break - September 20th to October 6th  

 

9

October 9th

Multiplexed reaction monitoring

10

October 16th

Protein interactions

11

October 23rd

Glyco-proteomics

12

October 30th

Phospho-proteomics

13

November 6th 

Spare

 

 

Q. Why no workshop in week 1?

A. If we had a workshop session on that day, the students presenting their research papers would have no time to prepare. If we start workshops in week two, then the first students will have sufficient time to prepare, which will 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 http://www.mq.edu.au/about_us/offices_and_units/information_technology/help/

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 redesigned practical class experiments. 

Updated and revised assessment tasks and descriptions to fit with the new three assessment policy.

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.


Unit information based on version 2025.07 of the Handbook