Nothing (nether chromatography peaks nor statistic graphs )showed up after transition list and results were imported.

Nothing (nether chromatography peaks nor statistic graphs )showed up after transition list and results were imported. q zhang  2024-05-21 02:22

Hi, Skyline teams!
My LC-MS data is glycome from mice liver tissue. After I import my transition list (29 glycan precursors in MS1, and 21 fragment under each precursors in MS2) and raw data, there's nothing showing up in the window. There's nothing in chromatography, peak area graph and retention time graph. Please see the screenshot in the word file I attached.
I was guessing this issue might be due to too much glycans in transition list, so I deleted 4 glycan precursors in MS1, 25 glycan precursors left, and start with a new skyline file with the same setting and importing steps. Then, it worked, and everything showed up.
However, I think I still need to figure out the solution, and want to know how can it work by using my originally complete transition list.

Nick Shulman responded:  2024-05-21 07:59
I do not know why things would look that way but if you send us your Skyline document I could figure it out.

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

Files which are less than 50MB can be attached to these support request. You can always upload larger files here:

Usually with a bug like this the problem turns out to be that there is one item in the list that is messing everything up. That is, Skyline is trying to display an average value and there is a single infinity in there that causes nothing to be able to be displayed.
After I see your Skyline document I will probably be able to figure out what is going wrong.
-- Nick
q zhang responded:  2024-05-21 08:26
Thanks for you reply! The file has been uploaded to your link.
Nick Shulman responded:  2024-05-21 08:52
Thank you for sending that Skyline document.
This is a bug in Skyline.
If you have more than 100 precursors selected then Skyline tries to show you only the 100 precursors with the highest peaks.

The bug is that if the 100th highest peak has a height of zero then you end up seeing the blank graph like this.

I will fix try to fix this bug soon.
-- Nick