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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?

Thank you!

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?

Thanks!!

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I would defninitely go with a custom background which should be all the proteins that were actually measured in your experiment since you should only take into account what was measured.

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