Monday, March 18, 2013
Proteome Discoverer 1.4 vs MaxQuant 220.127.116.11
Here is my vindication, though! To celebrate last week's release of Proteome Discoverer 1.4, I took a very nice SILAC labeled data set and ran it through PD 1.4 and MaxQuant 18.104.22.168 (the newest iteration, as of this posting date).
Dataset: Human cancer cell line passaged in SILAC media with Lysine (6) and Arginine (10). The data was analyzed in one go on a Q Exactive system on a 180 minute gradient using a Top20 approach. ~600 MB file.
Dynamic modifications: Carbamidomethylation (C), Oxidation (M), N-acetylation, and SILAC labels
MS1 tolerance: 10 ppm (20 ppm first search for MxQ, 10 ppm for second)
MS2 tolerance: 50 ppm
FASTA: IPI Human 3.77 (originally downloaded from maxquant.org)
MaxQuant used Perseus 22.214.171.124 with an FDR of 0.01 and implemented 4 threads
PD used Sequest with the Percolator algorithm at default parameters
PC: AMD Quad Core, clocked at ~3 GHz with 8 GB of RAM
Total search time:
MaxQuant: 109 minutes
PD: 23 minutes
MaxQuant: 425 total grouped IDs, 27 of which were contaminants and 12 were reverse sequences.
386 human protein IDs
465 grouped proteins
I'll be honest. I was scared at first. MaxQuant has gone through some significant revision since I was last using it commonly. Some of the new features, such as the ability to go back and re-search spectra are crazy impressive. That team contains some of the best researchers in our field and continues to innovate how we do proteomics and process MS/MS data. However, I have met a lot of the team that writes PD and they are no slouches either.
I'm going to throw in a caveat here: I am an expert at using Proteome Discoverer. I've been using PD since version 1.0 and have been using the beta versions of PD 1.4 for about 6 months. I'm less adept with MaxQuant. For a quad core cpu, I don't know how many threads would be optimal. 4 seems the smartest, but I may have been able to optimize that number and sped it up (virtual threading, or whatever...) It may also be possible to optimize first search/second search parameters to gain more IDs. Would I have picked up almost 100 quantifiable IDs? I doubt it, but maybe the disparity wouldn't have been as large.
In time, I might do a follow-up article to this one. It would be nice to see what the overlap in ID and/or quan is like. It is a little difficult due to how differently MaxQuant and PD deal with protein grouping. My guess, however, is that the majority of IDs and quan are the same, but that Andromeda and Sequest would each add complementary data to each other.
But for now, for just pure depth of coverage and quan, Proteome Discoverer appears to be the winner, though I'd still encourage you to try running both. The worst that would happen is that you'd get more data from that MS/MS experiment.