Importing Sciex Results from 2 Periods (pos/neg)

Importing Sciex Results from 2 Periods (pos/neg) dawn dufield  2018-12-10


I have an experiment where I have collected pos and neg data in 1 file in 2 periods. When I try to import that data to review in skyline. It appears to only see the first experiment (pos) and shows no data for the neg ion transitions? Is there a way to be able to look at all the data from the file within skyline?


Nick Shulman responded:  2018-12-10
It sounds like Skyline might have a bug in it.

Can you send us your files?

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files, including extracted chromatograms.

You should also send us at least one of your .wiff files (and the .wiff.scan file that goes along with it).

If those files are less than 50MB, you can attach them to this support request.
Otherwise, you can upload them here:
-- Nick
dawn dufield responded:  2018-12-10
ok thanks... uploaded the skyline file and the wiff files
Brian Pratt responded:  2018-12-10
Hi Dawn,

It's just a small problem with your transition list.

Skyline won't search the negative data for positive transitions (or vice versa), and all your transitions are positive. For example "GM3 Neg" has charge +1 instead of -1.

Fix that and you should find that it all works as expected.


Brian Pratt
dawn dufield responded:  2018-12-10
Great thanks.....
dawn dufield responded:  2018-12-10
Is there an easy way to modify the charges or do I need to import them again?

Brian Pratt responded:  2018-12-10
That's not an editable property, you'll need to reimport at least that part of your transition list (after first deleting the incorrect targets).
matt.chambers42 responded:  2018-12-14
Brian did you delete the uploaded file? I've never seen a WIFF with multiple periods before. Will be useful for testing.