Incomplete MS1 XIC in case of additional ms/ms filtering

Incomplete MS1 XIC in case of additional ms/ms filtering Fabian  2018-05-08

Dear all,

I,ve encountered an issue when trying to load MS1 and MS2 XICs into skyline.
The method is dd with an inclusion list on a Q-Exactive HF.
I would like to see the complete MS1 XIC, therefore I set "Include all matching scans" in "Transittion settings" in the "Full Scan" tab.
This works well in case no MS/MS filtering is included, however setting "MS/MS filtering" to "target" to include the ms2 informations, the first and last ms2 are used as the borders for ms1 and ms2 XICs.
This is rather unpleasant for my purpose and seems to influence ms1-based quantification as well, as one might interprete from the attached figure

In case of only 1 ms2 is present, the ms1 trace is complete, but the ms2 XIC looks pretty odd.

Many thanks in advance


Nick Shulman responded:  2018-05-08
Skyline truncates the MS1 chromatograms because that is the correct thing to be doing in the case of a scheduled PRM experiment, where you have explicitly told the mass spectrometer to collect MS2 scans over the time range where you expect the peptide to be eluting.

We have had a couple of complaints where Skyline does this for DDA data:

I think we could give you more control over this. Specifically, I am thinking that we should make it so that if you have marked all of your MS2 transitions as non-quantitative, then Skyline should not truncate the MS1 chromatograms like this.

I will try to make this change and get it into the next update of Skyline-Daily.
Fabian responded:  2018-05-14
Dear Nick Shulman,

Thank you so much for your fast response!

I understand the logic behind truncating the MS1 chromatogramm in case of a scheduled PRM experiment.
Nevertheless even in such cases it is sometimes pleasant to observe the complete MS1 trace.

Yes, having more control as a user would be highly appreciated, thanks!
moritz voelker-albert responded:  2018-07-17
Dear Nick Shulman,

I was wondering, whether the above mentioned MS1 chromatogram truncation has been fixed. I still encounter the problem and would be very happy to get a tool to control for it.

Many thanks in advance and all the best,

Nick Shulman responded:  2018-07-17
No, these proposed changes have not happened.
Probably what we are going to do instead is add a new "Acquisition Method" to "Settings > Transition Settings > Full Scan".
Currently we have "None", "Targeted" and "DIA". We a planning on adding "DDA", which, among other things would prevent this sort of truncation, but also would cause the MS2 chromatograms to be ignored for the purpose of peak picking, quantification, etc.
mmaust responded:  2019-01-22
I was wondering if there was ever anything done with the DDA situation that you mentioned? I'm interested in using this for a system suitability workflow with some peptide standards.
Nick Shulman responded:  2019-01-22
Hi, mmaust,

Yes, if you use Skyline-Daily, then you can choose "DDA" as the MS/MS Filtering Acquisition method on
Settings > Transition Settings > Full Scan

When you choose "DDA", Skyline will extract chromatograms for the MS2 scans which isolate the precursor, but those MS2 chromatograms will not be used for peak finding or quantification.

You can install Skyline-Daily here:
-- Nick