Today I did the Applications of mass spectrometry-based proteomics in research workshop. I did a similar workshop last year but at that stage I had no idea what proteomics was. At least this time round I had a better idea and most of the presentations on the new proteomic platform (Pierre Faou), types of proteomic tests available (Rohan Lowe) and LC-MS proteomic bioinformatics and visualisation (Harinda). I found the course very useful in getting some initial ideas beyond just comparing the protein abundance between PD and controls.
I have set up a Zoom meeting with Rohan Lowe for Wednesday 1st July at 10am to go over the following questions:
- Research area: I think my main area is Post Translational Modification, id this correct?
- Peptide Mapping:
- Can the mapping be done on a comparative basis?
- If not which technique would I use to compare the mitochondria in leukocytes between Parkinson's patients and healthy controls?
- Abundance depletion:
- With the new faster technology, would we still need to deplete the blood samples to lower the high abundance proteins such as albumin and globulin to make the low abundance proteins easier to detect?
- If we deplete the sample, will the remaining low abundance proteins need to be enriched? If so how would we do this with human blood samples?
- Pierre mentioned you always run a sample test before the full proteomic analysis. What sort of sample should we think about?
- Protocols:
- What is the process to identify the key experimental steps that enable the correct protocols to be identified?
- Validation: How do we confirm the proteomic results are accurate - is there a validation process?
- Chris Adda mentioned LTU research was subsidised - how does this work?
- Bioinformatics: How is the relevant analysis derived? Does the proteomics team suggest the most appropriate analysis and does this as part of the proteomics package or do I do the analysis on line with software you give me access to?
