Sunday, March 31, 2013

MaxQuant and QE phosphoproteomics data

This is going to sound more like a gripe than what I mean this to be, but has anyone out there tried to process QE AIF-NL-ddMS2 data with MaxQuant?  Holy cow.  My server has been cranking at >90% CPU and/or hard drive capacity for 14 hours now to finish 6 files that PD 1.4 with SequestHT knocked out in <4 hours.  I'll take this to the MaxQuant Google group, but since there is no place in MaxQuant where you can filter out the AIF data from the MS2 data then that is where the hangup is.  I cancelled my SIEVE and PD queues just to allow MaxQuant more power, but it doesn't seem to have helped.

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