Hi there,

I'm very new to R and Proteomics in general so please forgive any lack of knowledge.

I have been given analysed mass spec data with protein hits given (Proteome Discoverer report from Thermo) alongside Area measurements and PSM counts. My experimental set up is a pull-down experiment, I'm trying to see if there are any potential interactors with our protein of interest.

However, to do a true comparison of conditions I need to normalise my experiments to something, and I'm unsure how to do this given the nature of the pull-down experiment (i.e: would be much easier if I was to compare treated vs untreated whole proteome analysis).

I have n=3 for untagged pull-down (to see if there's any common contaminants that stick to the pull-down), n=3 for tagged protein pull-down (to see any potential interactors) and n=3 for treated tagged cells (to compare with previous n=3 to see if this changes the pull-down proteome).

Do you have any ideas on where to start with this? Sorry if this isn't clear either, I can clear things up upon request.