(91572) Assessment 4: Practical Report
Produce a short technical report in a form consistent with proteomic journals covering the techniques, results and interpretation of your proteomics experiment in the practical classes. The report should be in the format of a short communication to a journal; divided into Introduction, Results and Conclusions.
Length: 2000-3000 words.
Due: Monday 28 October 2019
Criteria:The report will be assessed on your ability to
- Produce a document of a standard suitable for publication in a designated proteomic journal as a short communication (Professional skills and their appropriate application).
- Include an Introduction that clearly and concisely presents the experimental problem with reference to relevant current literature (Disciplinary knowledge and its appropriate application).
- Include Results that demonstrate the ability to present proteomic data in a discipline appropriate manner (Professional skills and their appropriate application).
- Include a Conclusion that demonstrates the level of expertise gained in Disciplinary knowledge and its appropriate application, Professional skills and their appropriate application and Communication skills, and will evaluate the results in the context of the published literature.
To provide more of a guideline of what you should include in your report. PLEASE NOTE: This next section is a GUIDE. It is NOT a template to be followed to the letter. Use your own judgement as to what you should include and whether you should write MORE to demonstrate your knowledge and understanding.
- In order for the assessors to assess whether or not you have a deep understanding of proteomics in general and of your data, you MUST show the assessors that you understand. Do not assume that your writing will be interpreted by the assessors in a different way to what is written. The assessors can only read what you have written NOT what you intended to say. Be clear and include all of the information necessary to demonstrate your understanding.
- The introduction should provide a small amount of detail about Escherichia coli to establish some context for your report. But the majority of the introduction should describe what is the purpose of analysing a proteome, what are the difficulties encountered when trying to analyse a proteome, how different techniques and technologies can be applied to analyse a proteome, and how quantification of a proteome can be performed. The introduction should end with the aims of the experiments being performed, the main aim being ‘what was done to the treatment sample?’ (but you can word this better).
- Methods. Rather than writing a traditional methods section detailing exactly what you did, your methods section should detail which methods were used and WHY they were used with a focus on how the methods can generate overlapping and complementary data. For example, you performed two separate protein extraction methodologies. WHY was this done? What was the benefits of doing separate extraction methods and why not do just one?
- Results. There are two parts to this section.
- You MUST present your own results that you generated. The results of your assays. Your 1D-PAGE images. Your 2D-PAGE images. Your gel images should be labelled to obvious changes in protein abundance and these should be discussed in the text. A summary of your LC/MS/MS data as analysed by Peaks and Mascot, noting any differences. If you were able to performed quantitative analysis, the results of these should be presented. If any other bioinformatic interpretation has been performed (for example, pathway analysis) this should be reported.
- If necessary, you can use the data generated by the demonstrators to perform quantitative analysis to produce a list of proteins that are changing in abundance. This list can then be used to answer the questions you set out in your aims. You must list the fold changes in abundance of the proteins that you use as evidence to support your view of what the treatment was.
- Discussion. This can also be broken up into a few sections.
- What was the quality of your data like? What steps could you use to improve the data? What additional work, using the current methodologies, could you perform to improve the data quality and reproducibility?
- What was done to the treatment sample? What is the evidence for this conclusion? How sure are you of the conclusion? What further experiments would you perform to be more certain?
- Were the methods used to generate the data appropriate? Why or why not? Did they produce overplapping, complementary data?
- Conclusion. Wrap everything up concisely. Summarise what you wanted to know, how you went about finding out, whether the analysis is robust and what the data says.
- All of the above should include proper referencing where appropriate. It is not appropriate to say ‘because Matt/Joel/Iain said so’ or ‘it is written in Canvas’. Find appropriate references to support your statements.
- In every section, you need to demonstrate critical thinking and understanding. Show the assessors your knowledge.