Skyline visualization bugs

[Apirog9]

Hello, I have found several problems with skyline visualization of results:

• if .dia files are used, it attempts to load them into skyline. Replacing them by .mzml in raw data window fixes problem. wold be good to loog for .mzml files in data directory.
• in skyline settings , mass accuracies for MS1 and MS2 seem to be reversed.

Artur

[vdemichev]

Hi Artur,

• Yes, it does not work with .dia, need to use the original raw files. This unfortunately will not be fixed in the future as Skyline just does not support those.

• These are fixed, i.e. since Skyline will not apply same mass correction as DIA-NN, it makes sense to use fairly wide generic mass tolerances.

Best,
Vadim

[Apirog9]

Hi, what I actually saw was settings in DIANN to 5ppm MS1 mass accuracy and 30ppm MS2 mass accuracy. In skyline I've got 30ppm for MS1 and 5ppm for MS2, which obviously messed up chromatogram extraction.

[vdemichev]

Oh, my error, correct. Thank you spotting this!!!