Are you running DIA IM-All ions on the 6560 IM-QTOF? I was testing the new version (4.60) for lipidomics and it looks faster than the previous one for IM data (I did not transform the data to .ibf, just drag & drop the files). However, I could only match CCS values with the lipidomics database. The precursor-fragment deconvolution did not work for such datafiles. I am wondering if there is an additional step for DIA IM-All ions for precursor-fragment deconvolution...
I have the same problem when trying to run in lipidomics mode... I run my lipidomics data in metabolomics mode and it suddenly worked. Maybe it is something related to the identification part. I am not sure.. but I think that is the only different part between them.. Since I use MSDial only for peak picking and alignment, I don't think it is a problem to use metabolomics mode.
I was wondering if there is a specific range minx for number of threads in MS Dial 4. I work in a workstation with 20 cores 2.2 GHz(2 processors) x64. I don't know exactly how to translate my CPU power threads to MS Dial threads. I usually use 3 threads.
