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Hi @vdemichev , after went through the NM paper, I got the following questions: 1. Does DIA-NN remove b1, y1, b2 and y2 ions when it determines fragment ions to...

What type of custom fragment ions do you want for annotation?

It works well if open the GUI through command line in Mac system: **java -jar PDV-2.0.0.jar** .

We haven't tested the pepXML and mzXML from PEAKS Studio. It looks PEAKS Studio can export mzIdentML which is a more standard format. Could you give a try using mzIdentML...

If you can share the pepXML and mzXML files with us, we can do a test on the data.

Could you share the files with us by dropbox or google drive?

PEAKS Studio can also export MGF. We could try MGF to see if it works