I've almost got it but I have to go home. So maybe you'll see something obvious before I get back.
I made two changes to Tandem.pm
1. My system did not have $TMPDIR defined so I hard coded /tmp/ instead.
2. In PATH=/share/apps/cpas/bin/tpp/bin:/share/apps/cpas/bin/:/usr/local/bin:${PATH}, the colon slash before usr/local/bin/ was missing so I added it.

It gets right to the end and then Protein Prophet lets me down. Files attached.

Thanks,
Bill