Sunday, April 7, 2013
Early impressions on MSAmanda vs. Sequest and Mascot
I'll save the sample processing details for the manuscript, but I will say that this is actually not a very fair comparison for MSAmanda. This is because of FDR. On Sequest HT and Mascot, Percolator gave me a significant boost, giving me 20-40% more peptides than using a simple 1% FDR. For some reason I haven't investigated yet, searches of this data set on MSAmanda with Percolator do not complete. So this is MSAmanda with a 1% FDR and both of the other data sets boosted with Percolator cutoffs.
If you use 1% FDR on all three of them: MSAmanda wins by far, finding dramatically more peptides than either Mascot or Sequest. I am using the data above because I am more concerned with total peptides right now than dumping a lot of time into troubleshooting FDRs. I am a pathway-centric biologist, after all.
BTW, yes these numbers are low. When we see phosphoproteomics papers we like to see thousands of sites, there is a good reason for this, but I can't go into it without revealing what I'm working on.
Anyway! Download MSAmanda and instructions for installing it in Proteome Discoverer here.
UPDATE: 4/16/13: Scratch what I've said about MSAmanda and Percolator. It works just fine with Percolator. You simply need to make sure that you aren't ordering the same modification twice. I set Carbamidomethylation of cysteine as both a static and dynamic mod. That would error out just about everything.
Also, if you download MSAmanda now, it installs with no problems on Win 7 32-bit PCs. Again, it may have been my mistake. At the end of my incredibly long days I get to work on my own projects. Sometimes I'm really tired and sleepy by then....