Kind of. Using the digested proteome solved my problems of not having valid MS2 data. However, Sean reported that we’ve hit a new snag. It seems like the memory request argument isn’t a global memory request, but specifies memory for each instance of
pecanpie. Basically, the first instance takes up all of the memory and the following instances time out. Sean’s suggestion is to rerun
pecanpie and tell it to only look at three isolation windows concurrently as it makes its way down the isolation scheme.
Figure 1. #MOOD