Some bugs shown in software

Some bugs shown in software fenglinshen yzu  2020-10-13

Some peptides can't show the intact peak when we analysed MRM HR results using skyline which was the lastest released. Only three peptides were analysed with a 15 min gredient and 7.5 min-window was set. We also found the same scan data imported to the latest released skyline software showed only three transitions which was set as "full scan", and when the data was imported to earlier version, all of the transitions were shown. The details are shown in the attachments.

Nick Shulman responded:  2020-10-13
Can you send us your Skyline document and your mass spec (raw) file?

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

If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:

You should also send us the raw file that you imported the chromatograms from.
Which type of mass spectrometer did you use?

-- Nick
fenglinshen yzu responded:  2020-10-13
The related files were attached. MS data "myb01-06" was technical replicates and the setting parameters of LC-MS/MS were same. Not all of the peptides or MS data showed problems as mentioned above.
fenglinshen yzu responded:  2020-10-13
The related files are large and I have uploaded it at
Nick Shulman responded:  2020-10-14
Thank you for sending me your files.

I am not sure what behavior you think is a bug or might have changed.

Whenever you make a change to the set of Targets in a Skyline document, you need to tell Skyline to extract chromatograms again. Otherwise the newly added transitions will not have chromatograms.

One way to tell Skyline to extract chromatograms again is by going to:
Edit > Manage Results > Reimport

-- Nick