humble plea for peak boundary feature

humble plea for peak boundary feature Will Thompson  2021-06-21

Dear Brendan and Brian,

I have a plea for a feature that would save us a ton of time, and I hope would benefit many and would be pretty simple to implement. I would like to ask for a "Apply Peak Boundaries To All" feature in the right-click menu on the chromatogram window. I don't know what the back-end functionality of the "apply peak to all" or " subsequent" is, but it seems to be hopelessly broken and we spend a ton of time manually curating some peaks that have odd shapes or have not great S/N. My vision for this new feature is that if i integrate a peak and click the "Apply Peak Boundary To All" button, Skyline would just blindly apply those peak boundaries to that analyte across the document. No questions asked, no peak detection, just update the start and end time for the integration for every replicate in the document. Currently, in order to accomplish this task we need to integrate one replicate, then copy the table for the given retention time out from the doc grid, paste down for the replicates we need (make sure to not go too many replicates down!), save as a peak boundary file renaming key columns, then import the peak boundaries. The whole process seems such a waste of time for something that would seemingly be very easy to keep within Skyline. As with many things, I probably overestimate the simplicity but I hope it can be done. This would save us potentially hours in curation per plate of multiplexed quantitative metabolomics data.

Your humble beggar of features,


Brendan MacLean responded:  2021-06-21

Hi Will,
This came up recently in a call with another collaborator, and they even had a suggestion for how to implement it "Synchronize Integration", a mode like "Synchronize Zooming" in which you would get what you are describing, but it would always be possible to switch out of this mode to get what we have today.

Your feedback on this idea would be much appreciated.


Will Thompson responded:  2021-06-21

Hi Brendan

I think the implementation you are talking about would provide the functionality we are looking for, and whether or not you call it "synchronize" or "apply" peak boundaries matters not to me. One thing that may be worth thinking about is the mechanism which is easiest for the user to perform and most difficult for them to mess up. If turning on/off the 'synchronization' automatically applies to all analytes at once, that may provide a little less functionality than applying a specified set of peak boundaries on an analyte by analyte basis as the user defines. Another thing is that if the 'synchronization' could be easily unchecked by the user (and applies to all analytes even those that are not currently 'active' in the user view) it does seem like the user could undo it without knowing it. Just something to think about. Our normal workflow would be to look at a couple replicates of an analyte (such as a quality control sample in the middle of the queue), select the correct peak boundaries by checking integration and reintegrating as necessary, then preferably applying these boundaries to all samples. I can see how if 'synchronize boundaries' was selected, it would maybe save a couple clicks with this workflow.

Extremely pleased that this is being given this level of attention!



roman sakson responded:  2021-07-12

Dear Will, dear Brendan,

I do not have much to add, I just came across this thread and would like to stress that the kind of feature discussed above would be extremely welcome at my institute as well!


Brendan MacLean responded:  2021-11-03

Hi Will and Roman,
I just wanted to make sure you both saw the latest Skyline-daily release with synchronized integration. We would love to get your feedback on it at this stage.

Thanks for your interest in this feature.


roman sakson responded:  2021-11-08

Hi Brendan,

thank you very much for pointing this out, I have to admit that I have not tested the latest daily-release yet. It is slightly more difficult to work with daily in our IT-environment but I am sure that I can make daily run as well. I will try to come back to you next week regarding some feedback.

Thank you for keeping Skyline flexible :)

roman sakson responded:  2021-11-20

Hello again,

as promised, here some preliminary feedback for this new (very cool!) feature:

In my test document, I had a few replicates and also some conditions. When I clicked on "Synchronize Integration..." for the first time, all replicates were checked per default. As I then went to Conditions via the "Group by:" dropdown menu, also all conditions were checked. I unchecked one and switched back to "Replicates" via the dropdown menu. My expectation was then now all replicates from the unchecked condition would have been unchecked while the rest would have remained selected. However, now all replicates were unchecked. Switching back again to the Condition list, I saw then now also all conditions were unchecked. All in all, it seems that the feature expects me to stay and work exclusively within replicates or within conditions but once I use the dropdown menu to switch, all previous work is gone. There seems no major harm in it as I can always cancel, it's simply unexpected... Does it have anything to do with the new "Group Apply to By" feature that is available when synchronize integration is off (probably essentially the same functionality, isn't it)?

Thank you,

Kaipo responded:  2021-11-22

Hi Roman,
Thank you for the feedback. This behavior will be updated to keep your selections checked when switching between groupings.


roman sakson responded:  2021-11-22

Thank you!