Unit convenor and teaching staff |
Unit convenor and teaching staff
Unit Convenor
Paul Haynes
Contact via paul.haynes@mq.edu.au
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Credit points |
Credit points
4
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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
The 4 credit point unit CBMS733 outlines chemical principles underlying the most recent developments in protein science. CBMS733 is co-taught with CBM8733 which is a postgraduate unit for students in coursework Masters degree programs. The unit extends previous work undertaken in CBMS732, which included an understanding of the emerging new disciplines of proteomics, structural biology and bioinformatics. There is no formal prerequisite to complete CBMS732, but it is desirable. CBMS733 focuses on the proteomic methods used in the biotechnology and pharmaceutical industries to isolate, characterize, analyse and purify proteins using advanced proteomic technologies. The practical includes 1D and 2D protein gel separation, in-gel digestion of separated proteins, mass spectrometric analysis, database searching for protein identification, and shotgun proteomic quantitation.
The specific postgraduate learning outcomes are focused on understanding current scientific literature in the field of proteomics. Students are required to research an essay topic based on an analysis of relevant literature, and present their work as a scientific review article suitable for publication. In addition, the practical laboratory report is required to be analysed and presented in a format suitable for publication.
CBMS733 is offered internally in second semester only. There are two hours of lecture time and two hours of tutorial time per week, plus a five full day practical component taught during semester break
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Unit description |
Unit description
Functional 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 the use of drug treatment, or genetic or environmental intervention. This unit covers the principles and applications of functional 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; characterisation of protein post-translational modifications including phosphorylation, glycosylation and others; and application of proteomics in the pharmaceutical industry. Students must attend a compulsory one week laboratory session during the semester break.
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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:
Name | Weighting | Hurdle | Due |
---|---|---|---|
Mini-Review Essay | 15% | No | Friday September 6th |
Oral Tutorial Presentation | 15% | No | from week 2 onwards |
Continuing assessment | 5% | No | weekly |
Mid-semester test | 5% | No | week 8 |
Practical Report | 20% | No | Monday October 21st |
Final Exam | 40% | No | examination period |
Due: Friday September 6th
Weighting: 15%
Mini-Review Essay (Due 9am Friday September 6th) - 15%
Topic: Compare and contrast the way in which proteomics studies are performed in current literature as opposed to those performed ten years ago.
Due: from week 2 onwards
Weighting: 15%
Oral Tutorial Presentation – Various Dates 15%
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Note that for 2019, due to class numbers, the task definition has been modified so that the presentations can now be done in groups of up to a maximum of two people. If you want to work with a partner you can, or if you prefer to do it as an individual task you can do that too. Note that both students in a group need to take part in the presentation, so you can not use this as a way to avoid standing up in front of the class
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Due: weekly
Weighting: 5%
Continuing assessment: Weekly Speaker Questions 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.
Due: week 8
Weighting: 5%
Mid-semester test – Week 8 - 5%
Due: Monday October 21st
Weighting: 20%
Practical Report (Due Monday October 21st) - 20%
Due: examination period
Weighting: 40%
Final Exam (2.5 hrs, date and time to be advised), 40%
2.5hr exam covering all practical and theoretical components of CBMS733
Questions are a mix of long and short answer questions
CBMS833 Functional Proteomics
Other important items
LECTURE, TUTORIAL and PRACTICAL TIMETABLE
Lectures: Mondays 12:00 pm - 2:00 pm July 29th - November 4th, 9WW 102
Tutorials: Thursdays 12:00 pm - 2:00 pm, August 1st - November 7th, 3IR G240
NOTE: the first scientific content lecture will be held in the first tutorial timeslot, Thursday August 1st 12:00 pm - 2:00 pm in 3IR G240.
Practicals: Are held in a one-week block during semester break. You must be available for all of September 23rd- 27th. Practical classes run all day, approximately 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 Mondays 12-2pm, starting July 29th, 9WW 102
Week |
Date |
Lecture Title |
1 |
MONDAY July 29th |
Subject Outline, Introduction and Assessment Process, and General Introduction |
1 |
THURSDAY August 1st |
Mass spectrometry fundamentals (in tutorial timeslot) (3IR G240) |
2 |
August 5th |
Protein Identification from MS data |
3 |
August 12th |
2D gels and 2D DIGE |
4 |
August 19th |
Differential display and shotgun proteomics |
5 |
August 26th |
Quantitative proteomics (I) label-free |
6 |
Sept 2nd |
Quantitative proteomics (II) isotope labels |
7 |
Sept 9th |
Data dependent acquisition (DDA) and Data independent acquisition (DIA) |
Practical: 5+ Days, 23rd- 27th September (during semester break) |
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8 |
Sept 30th |
[Post practical data analysis] |
9 |
October 7th |
Multiple reaction monitoring and proteomics validation |
10 |
October 14th |
Protein-Protein Interactions |
Practical report due 9am Monday October 21st |
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11 |
October 21st |
Post-translational modifications (I) - Glycoproteomics |
12 |
October 28th |
Post-translational modifications (II) - Phosphoproteomics |
13 |
November 4th |
Revision |
All written work must be submitted through iLearn Turnitin. In addition, hardcopies of assignments and practical reports are to be handed in at the Departmental office in 4WW and are due in by 9am on the due date.
TUTORIAL TIMETABLE
Tutorials: Thursdays 12-2pm from August 8th
Room 3IR G240
Week |
Date |
1 |
[note: August 1st is used for a lecture] |
2 |
August 8th - MS Fundamentals |
3 |
August 15th - Protein ID |
4 |
August 22nd - 2D Gels and 2D DIGE |
5 |
August 29th - Shotgun proteomics |
6 |
September 5th - Label Free quantitation |
7 |
September 12th - Quantitation with labels |
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Semester Break - September 16th to September 29th |
8 |
October 3rd - Data Independent Acquisition |
9 |
October 10th - Multiplexed reaction monitoring |
10 |
October 17th - Protein interactions |
11 |
October 24th - Glycoproteomics |
12 |
October 31st - Phosphoproteomics |
13 |
November 7th (spare) |
Macquarie University policies and procedures are accessible from Policy Central (https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policy-central). Students should be aware of the following policies in particular with regard to Learning and Teaching:
Undergraduate students seeking more policy resources can visit the Student Policy Gateway (https://students.mq.edu.au/support/study/student-policy-gateway). It is your one-stop-shop for the key policies you need to know about throughout your undergraduate student journey.
If you would like to see all the policies relevant to Learning and Teaching visit Policy Central (https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policy-central).
Macquarie University students have a responsibility to be familiar with the Student Code of Conduct: https://students.mq.edu.au/study/getting-started/student-conduct
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
Guidelines for preparation of written work
ALL WRITTEN WORK MUST BE ORIGINAL. Students are sometimes tempted to use material which is not their own without due acknowledgment. This constitutes cheating, the penalty for which is failure of the course. It is considered equivalent to cheating in an examination. Direct copying and/or submitting material from your own work done in previous years is also considered cheating.
WHAT CONSTITUTES CHEATING?
Collusion
Collusion is the secret and fraudulent production of identical or superficially altered work submitted for assessment by two or more students. It is easily detected by the examiner from the similarity in styles. This constitutes cheating and will be dealt with accordingly.
Plagiarism
Plagiarism is the verbatim use of someone else's work, as if it were your own. This also constitutes cheating and will be dealt with accordingly. The "someone else" concerned may be an author, critic, lecturer, or even a fellow student. Plagiarism includes copying of material from practical books obtained from other students in the same or previous years. It also includes the direct copying of material from texts, references and other sources. It is important to realize that it does not make it acceptable to reproduce a sentence or paragraph from a published source when you add the name or number of the reference at the end.
If you need to quote another piece of work, do it correctly. You must provide quotation marks around the quotation and this must be referenced. In other words, the only proper way to indicate that the words are not yours is to show clearly that they are a quotation.
It is often desirable and may even be necessary to use other people's ideas but you must not pretend that they are your own. In such cases, your text should include a reference to the source of the idea. You may need to use a figure or table from another source. If so, the legend must indicate the source, with the appropriate reference. The list of referees should include acknowledgment of ideas, data and direct quotations from all sources.
More information regarding the University policy on academic honesty can also be found at http://www.mq.edu.au/policy/docs/academic_honesty/policy.html.
Collaboration
Students are often required to work cooperatively in groups when performing experiments. This may be necessitated by limitations on the amount of equipment or experimental material available, or simply by the fact that more than one pair of hands is required to do the experiments. Such collaboration is common and is an essential part of scientific endeavour. However, collaboration must always be acknowledged.
When you perform experimental work as part of a group, you must always acknowledge the collaboration by writing the names of the other members of the group at the start of your practical report.
Collaboration in performing an experiment does not extend to writing a report on the experiment where that report is assessed for marks. Students must prepare their own report individually.
Guidelines for preparation of written work
WHAT IS REQUIRED?
References
Essay and practical reports need scientific references to support facts and ideas that you are referring to. These should be primarily journal articles from recent scientific literature. You should only rarely need to cite textbooks; everything in a textbook was most likely published elsewhere in the literature long before the book was published. You should not refer to websites such as Expasy or NCBI for general information; gel images in Expasy for example, have also been published elsewhere in the scientific literature. You should NEVER refer to Wikipedia or to tutorial information posted on the web at another university. The reason for these rules is that textbooks, websites and Wikipedia are not primary sources, they are compilations of previously published material. More importantly, they are not peer-reviewed (including textbooks) so the authors can say whatever they like on a topic whether it is right, or not.
Learn to use Endnote or a similar program to manage and cite your references. This will make your written work look more polished and will avoid simple mistakes which cost you marks. Endnote is available as a free download from the MQ library, along with simple online tutorials in how to use it. Format references in your work according to the guidelines of any of the following journals: Analytical Biochemistry, Journal of Biological Chemistry, Journal of Proteome Research, Molecular and Cellular Proteomics, or Proteomics. The most common error students make with references is that the references in a list are inconsistent in style – they all need to be exactly the same format.
What is an essay?
An essay is a written discourse on a topic. It has a defined introduction, middle and conclusion, and contains logical arguments that follow a clear sequence. An essay does not contain dot point lists, and does not need to contain subheadings. It can contain table and figures to illustrate a point. If these are copied from a reference it needs to state that explicitly in the Figure legend or table footnote. Tables and figures should be numbered sequentially in order of their appearance in the text, and can either be inserted into the text or collated at the end. Every figure needs an explanatory legend, most tables need a footnote or two to explain the meaning of column headings. An essay has relevant references formatted as described earlier and collected at the end of the text.
What is a practical report?
A practical report has a title, aim, introduction, materials and methods, results, discussion, and references. It is divided into sections under these headings. It usually contains figures, and may contain tables as well. If these are copied from a reference it needs to state that explicitly in the Figure legend or table footnote. Tables and figures should be numbered sequentially in order of their appearance in the text, and can either be inserted into the text or collated at the end. Every figure needs an explanatory legend, most tables need a footnote or two to explain the meaning of column headings.
The aim of the experiment should be clearly stated. The methods should not just be copied directly from the course manual or notes. The results should describe what you observed, irrespective of whether you think it “worked” or not. Discussion should compare your observed results with literature or other experiments in class, especially if you have positive controls to work with. A practical report has relevant references formatted as described earlier and collected at the end of the text.
HINTS ON HOW TO USE SCIENTIFIC JOURNALS
During CBMS733 we will use current research (as distinct from partially digested textbook examples) to illustrate principles. The most up-to-date information is published in scientific journals.
CBMS733 students need to read journal articles to supplement the information given in lectures and practical notes. Your own reports should be modeled on the style of scientific papers (so take careful note of their presentation). It is important that you become efficient at using the large amount of information available. A huge number of journals and papers are available. The following paragraphs give you some guidance in doing this efficiently.
If everyone read scientific papers with care, effort and attention to detail, we would have to read a lot less. Develop an economical reading style and avoid too much rereading. In addition:-
1. Do not read through the paper from start to finish. A journal article is NOT a novel (though the results and ideas may be!). The various sections are there for good reasons.
2. Read and think about the Title. "Is the paper really about the subject matter I thought it was? Do I need to read it at all?"
3. Read the Abstract (or Summary) to confirm the suspicions formed in 2. This section should give you an idea of the main results and why they are important. Ask yourself: "Do I need to read further? Is this paper appropriate?" This is especially important if you have uncovered the reference in another paper or from Science Citation Index or Current Contents. Titles often suggest that the paper is more relevant than it really is.
4. If you continue, now read the Results. Examine the figures and tables. They should be self-explanatory. (This is something that you must bear in mind when you prepare your own report. Good captions and labels are vital). What do the results mean? How convincing are they? Now look at the Discussion. Do your interpretations of the data and conclusions agree with those of the author(s)?
5. How do these experiments fit in with the general research field and with current theories? In other words, why was the research conducted? This should be established in the Introduction.
Despite the efforts of editors and reviewers there are bad papers as well as good papers in the published literature. Some are badly presented, but contain basically good work. You have to plough through those to extract the gems of wisdom. Others look great on the surface but say nothing of importance. You should train yourself to recognize these quickly without wasting time on them. To help you here, look carefully at the following:-
(a) What are the hypotheses (or questions) posed in the paper? (Be careful that you are not simply forming your own idea of what the paper is testing.)
(b) What approach is used to collect the data (see Methods section).
(c) Do the data, and the manner of collection allow a DIRECT TEST of the hypothesis? If not, what sort of experiment would?
(d) Are there interpretations of the Results which you would make but which have been ignored by the author(s)?
You should try to bear these points in mind when you are reading any papers, but it will be especially important when reading the key papers for your reports, major essay and tutorial presentation. We expect that you will show evidence of having evaluated the strengths of published work.
TIMELY SUBMISSION
ALL CBMS733 assessment deadlines must be met
Late submissions will be penalised with 10% loss of the maximum mark for each day past the deadline.
If there is any medical reason why you cannot submit work on time or if you cannot give your tutorial topic for any reason, you should contact the course convenor as early as possible, before the due date.
Copies of medical certificates MUST be forwarded to the course convenor as soon as possible. Failure to do so will incur a zero mark for non-submission.
EXAMINATION POLICY
• As with all subjects in the Department of Chemistry and Biomolecular Sciences, your final mark has a large component of continual assessment.
• Since your final mark is the sum of all components of this subject, you should approach this subject in a consistent and diligent manner throughout the session; leaving your best effort to the final examination period would be most unwise.
• Remember, marks are deducted from the continuous assessment component if you are absent without cause or if your submissions are late.
• Despite the presence of a significant continuous assessment component in CBMS833, you will be required to reach a grade of 50% in the final exam in order to pass CBMS733. In the event you fail this unit, you can NOT request a supplementary examination or re-examination simply because you failed.
• The final examination is typically 2.5 hours long, but may be longer if required.
CBMS733 LABORATORY SAFETY POLICY
1. Laboratory coats and sensible fully enclosed footwear (no thongs or open-toed sandals) must be worn in the research lab at all times. Lab coats should be removed prior to entering common areas (eg: hallways, tea rooms).
2. Smoking, eating and drinking are not permitted at any time in any lab.
3. You are responsible for the smooth and efficient operation of your work area. Keep your assigned work areas as tidy as possible (e.g., clean and store any used items when no longer required; return any communal reagents to their assigned place in the laboratory). Do not leave a mess for someone else (eg: co-workers or Departmental technical staff) to clean up.
4. You might be handling bio-hazardous or radioactive materials during your practicals. Mouth pipetting is NOT allowed at any time. The Chemistry and Biomolecular Sciences Department has a complete Safety Manual which you may refer to at any time prior to undertaking a hazardous task. In order to provide a safe working environment, please take this request most seriously.
5. All instructions for the handling of:
(a) biohazardous and radioactive material;
(b) micro-organisms;
(c) recombinant materials; and
(d) research equipment
must be carefully adhered to.
6. Some practical exercises may involve the examination of human fluids, human cells or human cell lines. There should be no sharing of this material or any of the instruments used to collect them.
DISRUPTION TO STUDIES AND SUPPLEMENTARY EXAMINATIONS POLICY
The rules regarding special consideration and supplementary examinations are set out in full in the University Undergraduate Calendar. The following is a summary.
1. What is a request for Disruption to studies?
A request for the Department to take into account, when assessing your performance in any assignment or examination, circumstances beyond your control: typically medical problems or other compassionate circumstances. Forms regarding the Disruption to studies process are available at:
www.reg.mq.edu.au/Forms/APSCons.pdf
2. What are acceptable reasons for Disruption to studies?
(i) valid medical, compassionate and serious unforeseen personal events that prevent a student from meeting scheduled deadlines,
(ii) validated conflicts between scheduled assessments and sporting, cultural or other activities at a national or international level: these must be raised well in advance with the Department.
3. How do you apply?
(i) Lodge a written application, together with supporting documentation, with the Student Enquiries Office in Admin. Or do it online at ask.mq.edu.au.
(ii) Do this no later than 7 days following the serious illness or other situation. Admin. will pass it on to the Department.
(iii) It is your responsibility to check the outcome with the Department, not later than two weeks after lodging the application.
4. What is “supporting documentation”?
(i) A medical certificate, which states the date or dates of any relevant consultations or attendances, the nature of the problem and the treatment; and a specific statement that the student was unfit to complete the required assessment or examination on the date specified. Medical certificates which do not have all this information will not be accepted.
(ii) A letter from the University Counselling Service, or a professional counsellor, which sets out the general nature of the problem affecting the student, and the opinion of the counsellor that the student was unfit to complete the required assessment
(iii) A statutory declaration, setting out the facts upon which Disruption to studies is requested, and attaching any supporting documents.
Note: A letter from an employer, friend, religious advisor etc. is not sufficient.
5. Supplementary exams?
(i) These are granted only under special conditions: (a) if the student did not sit the standard examination for an acceptable reason; or (b) if the student, after reporting the illness to the Supervisor-in-Charge, left the examination room because of verified illness.
(ii) Early exam/assessment will not be permitted on the grounds of lengthening the period available for holidays or for departure overseas before the end of the exam period.
6. Timing of Supplementary Assessment
(i) Supplementary assessment is to be completed at a time convenient to the Department. It is the responsibility of the applicant to comply with the requirements of the Department.
(ii) It is your responsibility (a) to be available to sit for the exam at any time during the vacation period immediately following the application; AND (b) to leave a contact address and telephone number with the Department.
7. Form of Supplementary Assessment
Supplementary theory and practical exams may require different and additional assessment tasks to the normal examination. Supplementary examination may be in individual, oral format.
Macquarie University provides a range of support services for students. For details, visit http://students.mq.edu.au/support/
Learning Skills (mq.edu.au/learningskills) provides academic writing resources and study strategies to improve your marks and take control of your study.
Students with a disability are encouraged to contact the Disability Service who can provide appropriate help with any issues that arise during their studies.
For all student enquiries, visit Student Connect at ask.mq.edu.au
If you are a Global MBA student contact globalmba.support@mq.edu.au
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.
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This graduate capability is supported by:
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Reduced 2D gels and 2D DIGE to one lecture. Added an additional lecture on Data Dependent Acquisition (DDA) and Data Independent Acquisition (DIA). Revised and refreshed lecture content based on feedback from previous year, and updated tutorial paper list.
The 2018 lecture syllabus different to previous offerings. The two lectures presented previously on two-dimensional gel electrophoresis and two-dimensional differential in gel electrophoresis have been combined into a single lecture. An additional lecture has been added on Data Independent Acquisition approaches in shotgun proteomics. These changes reflect the state-of-the-art in the proteomics field, where Data Independent Acquisition shotgun proteomics experiments have become increasingly prevalent in the scientific literature.