Monday, February 20, 2012

Percolator vs Peptide Validator Part 2

So I finally had some free time to really look at Percolator vs. trusty old peptide validator.  This has been due to the fact that our Processing PC lost 3 hard drives (manufacturing defect, or my work simply kills PCs).  Since the next fasted PC I have access to is my home computer we built this winter, I got an emergency license from Thermo and loaded it at home.  Our PC is back with 2 new hard drives, but I'm still using my home PC to get caught up on the enormous backlog that we've generated.

Here is the experiment:  
1.) A single fraction (SCX separated) of mouse serum was ran on the Velos on a standard 140 min gradient using the Top10 method.
2.) This fraction was processed with Sequest and either Peptide Validator or Percolator using the manufacturer's default settings.  Each processing scheme was ran twice (alternating between schemes).

Peptide validator: 
Processing time:  7 minutes
Peptides:  216
Peptides, unique: 201
Protein groups:  61
Proteins total:  75

Processing time:  18 minutes
Peptides: 401
Peptides, unique: 381
Protein groups: 91
Proteins total: 120

I exported the peptide report to Excel:  Percolator found EVERY peptide that Peptide Validator did, and simply added 179 new peptides.

The next question, of course, is:  are these new peptides any good?

No comments:

Post a Comment