haianhle
commented
1 year ago Hi Vadim, I'm very new to mass spectrometry and proteomics. It appears that mass calibration is done using some nonlinear dependency between retention time, m/z, but also peak intensity. So I guess it makes total sense that when intensity is low (or also very high?), the mass calibration has trouble. We have been using max intensity instead of sum of intensities, but either probably would have resulted in the same issue. Any thoughts and comments on this would be greatly appreciated. Thank you so much Vadim. DIA-NN is a wonderful tool and we all wish we could understand it better to use it correctly.
Hi Vadim, we recently had some a few incidents where DIA-NN appears to take a very long time "Processing...". When the mass and MS1 accuracy are set to 10ppm then we get a message after a while that DIANN "Cannot perform mass calibration, too few confidently identified precursors". If we use DIA-NN's default mass accuracy, setting these values to 0, then we don't get this message but same thing otherwise. I attached the log files below. In general, could you please tell me what exactly DIANN is trying to do when it's "processing"? I guess it's doing peak assignments, but not sure in which scenario this likely happens just for diagnostic purpose.
In one case, the spectrum looks virtually identical to another that has no problem when we inspected the raw data using Bruker's Data Analysis software. The TIC traces for both MS1 and MSn were where they should be, but the intensity counts during infusion of ESI tune mix was half of what it should be. Retuning the detector and reflector appeared to fix the matter. In the other, we had tried a different set of diaPASEF windows resulting in a lot of MS2 signals and large data file. Thank you so much. Best wishes, Anh C5398.log.txt A8900.log.txt