Im using clusterProfiler for GO enrichment of differentially expressed proteins from different groups. It appears that most suitable is to use as a background for enrichment all proteins that "potentially could be in the lift of the differentially expressed proteins".
My issue is that I am not 100% sure what this means as I go though various rounds of selecting proteins before differential expression analysis. Eg I select only proteins quantified with >1 peptide.
Would you set the background for enrichment using really only the full list of proteins used in diff ex analysis (so the most stringently filtered ones), the list of proteins before filterin (so including proteons quantified with 1 peptide) or maybe even another list, eg the complete human proteome or the cells proteome as published by others before me?
Thanks a lot! Sebastian
ps: so far I am using the highly filtered list that includes only proteins used for diff ex analysis