I am doing a pathway enrichment analysis of a sets of proteins. Specific cell types (cardiospheres) were used to perform the experiment and for the quantification of proteins was used mass spectrometry. I am using gProfiler to perform pathway analysis, should I use custom background of all of those proteins identified from the experiment? or should I used without custom background?
UPDATE: Also, I am doing an enrichment analysis of the interactome of the set of proteins of interest. In that case should I used a custom background for the enrichment analysis or not?