March Seminar - Q&A

Post date: Mar 25, 2021 9:48:42 PM

There were a few questions at our March seminar that we didn't have time to relay during the meeting. See the responses to your questions here:

Questions for Professor Peter O'Connor

Q: How do you decide whether a data point is on a diagonal line or a vertical line?

We don't. The data is a 3D surface, and we can take any slice we like and project it on a 2D plot so that it looks a bit like a 'normal' MS/MS spectrum. If we see an interesting peak, it makes sense to take vertical, horizontal, and diagonal slices from there and see what we see. Of course, I showed the ones that show interesting information.

Q: Do you think it will work well and interpreting will be less complicated on model amino acid residues? I am working on methionines and, being a beginner in MSMS, I often have a hard time in analysing peaks in the conventional spectra.

Yes, it will work well for amino acids, particularly if you want to analyse them as a complex mixture. I'm afraid it won't simplify interpretation of the spectra however, that just takes practice. You should see the same types of fragment peaks as you do with a normal MS/MS experiment - perhaps with slightly different intensities.

Q: What possibilities are there to automate data analysis given the complexity of the data?

I think the automated data analysis prospects are extremely high. When we do the 3D peak picking, we get the MW of the precursor, the MW of the fragment, and the intensity as a 3D peak list (as an html or csv file) with very high accuracy in both dimensions, so data analysis algorithms will have excellent data to work from. We can already use Mascot peptide proteomics analysis with these peak lists, with a little re-arrangement and filtering of the 3D peak list. I suspect that there is a very large challenge for further statistical analytics and bio/chemoinformatics algorithm development going forward. But having good peak lists going in will help enormously.

Questions for Dr Robert Bradshaw

Q: Why the choice of cucumber?

This fruit has tight contact with the plastic packaging and it is an example of a fruit where people eat the skin. This seemed like the best model to prove our initial hypotheses, but we will be moving onto different types of samples in the future.

Q: Can you use this technique to quantitate the degree of contamination and use this to understand what the safety risk is from each type of phthalate?

Recent development in this area means that quantitative approaches are now possible using MALDI MS imaging, though it does come with a number of challenges. We will achieve quantitation using an LC-MS based approach of extracts from our sample.