eliminating contaminated fragment ions in DIA processing

eliminating contaminated fragment ions in DIA processing Tomas Vaisar  2021-05-25

Skyline team,
I wonder if there is a way to filter out contaminated transitions/fragment ions (on a large scale). I have run into many instances in processing DIA data that out of 6 top fragment ions some are clearly contaminated and often they are one of the higher ranked ones. Looking at mass accuracy they are clearly off (mass error >10ppm) while the rest of the fragment ions are spot on (<5ppm). Ranking clearly does not remove these. Sometimes they are just slightly shifted in retention or show a shoulder on the peak. I attach an example.


Nick Shulman responded:  2021-05-25
You can use the Document Grid to do things such as delete all transitions or remove all peaks that match a certain criteria.

To do this, you would create a Report which has the columns for the criteria that you want to filter on. After you have selected the rows containing what you want to remove from the document, you can use the "Actions" dropdown at the top of the Document Grid to delete Targets or remove Peaks.

-- Nick
Tomas Vaisar responded:  2021-05-25
Thanks Nick,
works like a charm.