text: user9010: 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!!
  
  user-1: 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.
  
original_text: 9010: <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>
   -1: <p>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.</p>
  