Applying manual integration windows when adding new transitions/fragments for an existing compound in Targets

Applying manual integration windows when adding new transitions/fragments for an existing compound in Targets Emmanuel  2020-07-27

Dear Skyline team,

I've manually adjusted the integration of a targeted small molecule across a dozen of samples and I'd like to add few more transitions/fragments for that compound (additional fragments found in another database than the first ones).

Is there a simple way to apply the manual integration boundaries to the new fragments without using the workaround of exporting/re-importing the peak boundaries as a report (as suggested by Tobi some years ago)?

When re-importing the results, it seems that the new transitions are integrated according to the default integration settings without taking into account the manual integration from the previous transitions. Therefore, I need to manually re-integrate all the samples ....

Thanks in advance for your help.


Nick Shulman responded:  2020-07-27
If you add new transitions to molecules that are already in your document, and then you reimport your results by going to:
Edit > Manage Results > Reimport
then your manually chosen peak boundaries are supposed to be preserved.

So long as you are using the "Reimport" button on the Manage Results dialog, we would expect the peak boundaries to be preserved.

It might be that something strange is going on. You can send us your Skyline document and we can take a look.

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

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:

You should also send us your raw file that you are reimporting results from.

-- Nick
Emmanuel responded:  2020-07-27
Dear Nick,

Please find attached a reduced dataset with 3 blank runs and 3 replicates of a pooled sample.

I did the manual integration of the first 4 transitions (prec + frags down to m/z 97). Then I've added 4 frags in the target list with the expected RT at 1.86 min without setting a RT tolerance window.
For the blank runs, the noise is integrated with the default settings, but not according to the manual integration boundaries previously defined. While for the pool the RT has shifted to 2 min and the 4 new transitions are not integrated at all (even after re-importing the results ...).

I'll send you the rawdata through the alternative large files url .

Thanks for your help.


Nick Shulman responded:  2020-07-28

Thank you for sending that file.

I see what you mean. If you add new transitions to precursors in your document, and those precursors have manually chosen peaks, then, when you do a reimport, the new transitions end up with null peak areas, similar to (but not exactly) what you would get if you had used the menu item "Remove Peak" to remove those new transitions' peaks.

I think the workaround that you have of exporting peak boundaries and reimporting them might be the best way to deal with this.

As far as I can tell, this has always been the behavior in Skyline, and I have never noticed since it's a rarer scenario than reimporting after adding new precursors or other settings changes.

I am not sure when we will be able to fix this in Skyline. Have opened this issue to keep track of the work item:

Thank you for reporting this issue.
-- Nick