Dear Skyline Team,

we are planning to use Skyline in the routine analysis of large Metabolomics experiments involving roughly 200 molecules and 300 replicates. From our testing Skyline is works well with that many molecules but is missing some features to make the handling of hundreds of replicates feasible. We’ve already looked at many of your great tutorials and answers in this forum but couldn’t find solutions for many problems we encountered. The following features would significantly improve the analysis of large numbers of replicates:

1. Most importantly the current viewing options for chromatograms are not well adapted for hundreds of replicates per molecule. We would suggest something like a scrolling window, where all chromatograms for a molecule can be scrolled through quickly. Another option would be to use the “View/Arrange graphs/Groups” feature to split all chromatograms over a handful of windows each with multiple tabs. It would then be very useful to advance through the tabs with one click in all windows simultaneously. This has already been requested here: https://skyline.ms/announcements/home/support/thread.view?rowId=60905
2. To more quickly evaluate and correct the peak integration bounds we heavily rely on the replicate comparison views for peak areas and retention times in combination with ordering by custom annotations (plate id, biological condition…). It would be great, if instead of the replicate’s filenames, Skyline would show the value of the ordering annotation on the x axis of replicate comparisons.
3. Finally it would be very useful to be able to change the order of chromatograms document-wide. Currently sorting the results grid or ordering the replicate comparison views doesn’t change the order of chromatograms in other windows. Being able to quickly click through chromatograms using up/down (or scroll as suggested above) in any desired order would make the manual peak picking for large numbers of replicates significantly more efficient.

Together with these features it would also be greatly appreciated if the bugs we found and reported here (https://skyline.ms/announcements/home/support/thread.view?rowId=71363), especially the “Synchronize zooming” feature, would be fixed. Thank you for your great software and active help in this forum!
Best

Simon