<p>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?</p>
<p>Thank you!</p>
<p>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?</p>
<p>Thanks!!</p>

<pathway><go-enrichment>
Pathway enrichment analysis with or without custom background
# Pathway enrichment analysis with or without custom background

(Asked by: username_0 on 2020-09-30)

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!!

**Tags:** pathway, go-enrichment

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## 0 answers

