DIA data from .d files

DIA data from .d files luzjpaulo  2021-10-05

Dear Skyline team,

I am having difficulty to open results files from a DIA experiment from a Bruker impact II .d files. When I try to import a DDA experiment it works well but once I switch to DIA the .d file is not recognized as mass espectrometry format. I would like to ask your help if possible.

Best regards
Joao Luz

Brian Pratt responded:  2021-10-05

Are you able to view the file in SeeMS (installs with msconvert, https://proteowizard.sourceforge.io/download.html)?

Best regards,

Brian Pratt

Nick Shulman responded:  2021-10-05
When Skyline sees a folder whose name ends in ".d", Skyline looks inside of the folder to see whether it contains a file named "analysis.baf" or "analysis.tdf". If the folder does not contain a file with either of those names, then Skyline will think that this is an ordinary folder with no mass spectrometry data in it.

What behavior are you experiencing in Skyline? If Skyline is not allowing you to choose the .d folder when you do "File > Import > Results", then I imagine that would be because there is no "analysis.baf" or "analysis.tdf" file in there. Or it Skyline telling you in some other way that this is not mass spec data?

Does your ".d" folder have a file with either of those names in it?

It might be helpful if we could see what files you do have. You can zip up the files that you have and upload them here:

-- Nick
luzjpaulo responded:  2021-10-06
Dear Mr Brian Pratt and Mr Nick Shulman,

Thank you for you time. I looked up in the folder and indeed there was not a baf file. I figured out that the problem was caused by some sort of trouble to download it. You helped me a lot.

Best regards,

Joao Luz
From Brazil