Proteome Discoverer 1.0, 1.2, and 1.3 comparisons

I finally got to sit down and run multiple datasets side-by-side on Proteome Discoverer 1.0, 1.2, and the new 1.3.
The results are pretty much what you would expect, but let me describe the data set:
-One run of serum taken from a mouse, depleted of the 4 most prevalent proteins (albumin, IGg, transferrin, and one other), digested, separated on a 240 minute gradient and ran using my standard Top10 CID method.
-All modifications were the same
-All cutoffs were the same
-The data was sent to both our Mascot server and the local Sequest program
-The default FDR was employed on both 1.2 and 1.3 (no FDR in PD 1.0)
Results:
PD 1.0:  408 protein IDs
PD 1.2:  121 protein IDs
PD 1.3:  275 protein IDs.

Wow, right?  I'm still investigating, but my hypothesis is:  PD 1.0 has a tremendous number of false positives.  Realizing this, Thermo added FDR calculations to PD 1.2.  These were so strict that they cut the data received dramatically.  PD 1.3 employs a new algorithm that is closer to the true peptide counts.

I will continue to investigate as I have opportunity.