I am working on centrosomal proteins. I overexpressed my POI and then I did SNAP capture pulldown followed by mass spec and I got approximately 700 protein hits. I am trying to validate specific centrosomal proteins out of those hits? I analysed my data through Protein Pilot? What all parameters should I take into consideration before selecting proteins for CoIP?
If we are using %Cov(95) scoring as a criteria, what should be the appropriate cutoff value? What does it mean if %Cov(95) score comes zero and can we still consider validating CoIP with that score? My maximum %Cov(95) value came around 5%.
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