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Bug reports regarding the handling of large amounts of replicates

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Bug reports regarding the handling of large amounts of replicates simow02  2025-07-22 06:11
 
Dear Skyline Team,

while experimenting with Skyline to potentially use it for the routine analysis of large metabolomics experiments, we encountered the following bugs:

1. The “Synchronize zooming” feature currently only works, if all replicates have been loaded once. It would be greatly appreciated if this could be fixed, so that the synchronization works without having to switch from tabbed to tiled chromatograms to load everything each time a new molecule is selected. This has already been discussed here: https://skyline.ms/announcements/home/support/thread.view?rowId=64947
2. To get an overview of many chromatograms quickly the technique of using the results grid and up/down arrow keys works great. But we did notice a bug, when clicking up/down it’s not possible to then immediately see the last chromatogram by using down/up. Just a minor thing but a fix would still be appreciated.
3. Maybe not a bug but when experimenting with the “File/Import/Annotations” feature we noticed that annotations of different types, e.g. replicates and molecules, can’t be imported in the same table. This seems to be because the column headers are type specific even if the respective cells are left empty. As we would need to routinely import annotations for replicates, molecules and transitions it would be great if all that could work with a single table.

We would greatly appreciate if these could be fixed Thank you for your great software and active help in this forum!
Best

Simon
 
 
Nick Shulman responded:  2025-07-22 07:14
It would be helpful if you could send us an example document with this many replicates.
Also, can you send us the text file that you used with "File > Import > Annotations"? It was certainly our intention that you should be able to use that feature with multiple types of things at the same time (just like "File > Export > Annotations" works with multiple types of things). It sounds like a bug might have crept in there.

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

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url

I don't understand exactly what you are saying for #2. Can you rephrase that?
-- Nick
 
simow02 responded:  2025-07-29 06:37
Dear Nick,

Thank you for your quick reply, we would like to share a Skyline document with you but the data privacy policy in our company makes this quite hard. There is already a document prepared for you which has been heavily adapted to meet the required standards, but the key issues should still be reproducible. This document includes GC-MS data from Agilent instruments, so we used the Skyline Tester version shared by Brian Pratt in this thread: GC MS Agilent import: /home/support, thanks so much for addressing these import problems! It would be nice if you could give us a mail address to more confidentially send the document too.
While the Skyline document waits for approval, we’ve already uploaded a csv with which the behavior we outlined in the third point of our original post can be reproduced. Thanks for looking into that.
Regarding the second original point, sorry to not have been clearer on that: When using the Results Grid and tabbed chromatograms, once a replicate is clicked, the one before/after it can be viewed by clicking the up/down arrow keys. But immediately after clicking up/down it is currently not possible to go back to the previous chromatogram by clicking down/up. Pretty sure that this behavior is not intended and it makes comparing tabbed chromatograms by toggling between them impossible.

Best

Simon
 
Nick Shulman responded:  2025-08-05 21:07
In the CSV file that you attached, there are a lot of places where there is a space character between two commas.
If you removed that space, then Skyline would not complain that the annotation does not apply to that particular element. But, when that space is there, Skyline thinks that you really do want to set the annotation value to a space character.
-- Nick
 
simow02 responded:  2025-08-08 06:27
Hello Nick,
thank you for pointing this out, removing the spaces fixes the problem.
Best
Simon