Biological Mass Spectrometry

BIO8206 Biological Mass Spectrometry | Section 3 Assignment

This assignment contributes 20% of your module assessment for BIO8206. It is marked out of 100 according to the Universitys Conceptual Equivalent Scale for Postgraduate Taught programmes.

Submission Instructions:

• Use of text generation tools (e.g. ChatGPT, Gemini, Copilot or similar) is not allowed in this assignment
• Ensure that your student number is written in the box above.
• Ensure that all the questions have been answered and that all graphs/tables/figures have been inserted into the appropriate part of the assignment.
• Ensure that you have not exceeded the word limit (where stated) for questions.
• Ensure that a reference section details any cited literature you have used in your assignment.
• You are free to choose your method of referencing (eg: Harvard or Numbered) but you must be consistent and conform to the requirements of the format.
• Save as a PDF file and submit to Canvas through the Turnitin portal.
• If you have any questions regarding this assignment, please post them to the Discussion thread on Canvas for Section 3 Assignment.

1. Protein sequences and theoretical digestion [15% of Assignment]

Each student has been assigned one protein to work on (see table below). Copy the UniProt accession number and search for this protein (https://www.uniprot.org/). Scroll down to the Sequences subheading.

1. Copy/paste the protein sequence into your report
2. Based on the uniprot page for your protein make some brief comments on what is known about this protein (e.g. features, disease association, interactions, domains, etc) [max 100 words]

Go the PeptideMass tool on the Expasy website (https://web.expasy.org/peptide_mass/). Generate theoretical digests of your protein with (1) trypsin, and for an alternative protease (2) Lys C, and list the peptide sequences and molecular masses [note: all setting should be default except set change mass bigger than to 1000 and switch off all known post-translational modifications]

3. Paste the theoretical digests into your report

4.From the results (or otherwise from literature search) determine what the cleavage rules for Lys C are (i.e. trypsin cleaves on the c-terminal side or lysine and arginine residues, what is the rule for Lys C ?).

[insert answers section 1 here]

2. Exploration of MS proteomics data in online repositories [35 %]

Navigate to the online proteomics data repository at the Global Proteome Machine Database (https://gpmdb.thegpm.org/). Search for your protein using the UniProt accession number. Click on the ENSP number of the first entry in the list to see how many times this protein has been observed in GPMDB. Next click on the first entry in this list by clicking P under model. This will bring up a list of all of the peptide sequences observed for this protein in this experiment. Click on the first peptide sequence to see the MS2 spectrum that the peptide was identified by.

1. Paste a snapshot of the MS2 spectrum into your report. Describe the key features of this plot (max 100 words)

Go back to the page after you searched the UniProt accession and now click on peps to bring up the diagram of observed AA residues for this protein.

2.Paste a snapshot of the Westmore-Standing (W-S) diagram into your report. Describe the key features of this plot and what you can understand from it (max 100 words)

3. Go back to the page after you searched the UniProt accession and now click on PTMs to bring up the diagram showing all observed post translational modifications for this protein. Describe the key features of this plot and what you can understand from it (max 100 words)

4. Paste a snapshot of the Modification-Abundance (M-A) diagram into your report. What kind of PTM is most frequently observed for this protein. Describe the key features of this plot and what you can understand from it (max 100 words)

5. Write a brief comment about the utility of mass spectrometry proteomics repositories such as GPMDB (100 words max)

3. Write a critique of one of the proteomics research papers discussed in the Proteomics section lecture 4 (length: 600 60 words). Alternately you may select a paper of your choice as long as the main analytical technique is mass spectrometry-based proteomics [50 %]

Note: pdfs of all 6 papers are available on Canvas in the Suggested Further Reading section of BIO8206 Proteomics Lecture 4 page

Recommended approach and structure:

1. Understand and explain (in own words) the advance in methodology or biology described in the research paper
2. Make some comments on the paper of the type:
   1. What are the strengths and weaknesses of the paper?
   2. Could the weaknesses be addressed with other experiments/analyses? How?
3. Can you suggest follow-up studies that could further advance the topic addressed?

Note: the key element of this question is to add some independent thoughts of your own. Avoid just restating the summary.