Hello everyone,
I have proteomics data from cell homogenate and different cell comparments from my Control (C) and treated (T) cells which I need to compare. I got unique peptide count and LFQ data for a list of proteins.
I need to compare first C vs T conditions of my homogenate so that I could choose the proteins which have not altered quantification (no expression change), and then compare the non-altered proteins in homogenate with the proteins in each compartment to see if they have changes in localization with my treatment in any of the compartments. Therefore, I need to calculate fold-changes and pvalues too.
I was following this paper (DOI: 10.1039/d0mo00087f) to perform normalization between C and T samples for homogenate and each comparment but I am not sure that I can compare then among different compartments.
What would be the best kind of normalization for my data?
Thank you.
