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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Skyline settings based on DIA-NN pipeline #1087

Open saradufour opened 4 months ago

saradufour commented 4 months ago

Hi!

I'm currently exploring the skyline add-on in DIA-NN (which is very cool, thanks for that!). I was wondering if there is a way that the Skyline settings are set based on the settings from the pipeline in DIA-NN? At the moment I noticed that the number of missed cleavages in the Skyline bat file is always 1 even if the number was set to 2 in the DIA-NN search. Another example is the precursor charge range. Default in DIA-NN it is set from 1-4 but the skyline bat file puts the setting from 2-6.

It would make the visualization even more powerful!

Best, Sara

vdemichev commented 4 months ago

Hi Sara,

Thank you for pointing this out. At the moment you can manually correct the .bat file that is being created by DIA-NN GUI to launch Skyline. In the future we will fix this.

Best, Vadim

saradufour commented 4 months ago

Hi Vadim,

Thanks for the very quick reply! Yes, we are doing is like this at the moment. Just thought it might be helpful to avoid misinterpretations. :)

Best, Sara