This evaluation is somewhat unfair to MaxQuant, due to the fact that I only have the 1.1 version operating. This is due to the fact that the Nature Methods paper has instructions for this software and updated instructions for the new version using their in-house Perseus search engine are not available.
For this comparison, 22 files containing SILAC-labeled samples were downloaded from the Tranche database.
The samples were from human cancer cell lines and FASTA employed was the same IPI derived FASTA available at Maxquant.org in the useful files folder (which they very nicely update frequently!)
All parameters within my power to control were made equivalent, including exclusively using Mascot for both searches
Results:
1) Quantifiable protein IDs: PD- 643, MQ, 311
2) Percent overlap (average): ~23% (identification)
3) In matching protein IDs, direction of regulation overlap: 100%
3) Time to process: PD ~ 9 hours, MQ, ~3 hours
Summary: There are definite pros and cons to each software package. PD takes longer, isn't free (unless it came with your equipment, which it often does), and comes up with more protein IDs. MQ is faster, free, has open source code so you know what it is doing (except for when it comes to Mascot) but doesn't produce as many IDs as PD. The best part is the number of unique proteins that come from using the two methods on the same dataset. If you have PD, you might want to download MQ (its free, after all!) and run your SILAC samples on it as well. It is fast and may give you more to work with!
Update: If you are interested in a more recent comparison, please follow this link to my analysis of Proteome Discoverer 1.4 vs MaxQuant 1.3.0.5.
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