From the journal Bioinformatics, we have:

PEPPER: cytoscape app for protein complex expansion using protein–protein interaction network

The bogus nature of this acronym is quickly revealed from the very first line of the abstract:

We introduce PEPPER (Protein complex Expansion using Protein–Protein intERactions)

Winning a JABBA award is one thing, but you get bonus points if you decide to use the same name as a completely different bioinformatics tool (something that is, sadly, becoming more common). So if you run a Google search for pepper bioinformatics, you may also come across a molecular visualizer called PeppeR.