diaPASEF data analysis

diaPASEF data analysis thsofia17681  2019-10-01

Hi I would like to ask you if you have a basic tutorial on how to import diaPASEF data and how to see the MS2 raw spectra of the files.
Please note I am pretty rookie on Skyline. I have taken courses but never used it extensively.

Brian Pratt responded:  2019-10-01

Our support for diaPASEF isn't officially released yet, but I'll contact you off list with information on how to get an advance build that does support it.

It's not any different from normal DIA handling in Skyline, other than needing to have ion mobility information to make use of the ion mobility dimension for reducing peak interference. What is your source for collisional cross section and/or inverse ion mobility values?

You can see the MS2 raw spectra by clicking on an MS2 chromatogram. The Ion Mobility Spectrum Filtering tutorial (https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ims) shows examples of this.

Best Regards

Brian Pratt