Skyline-daily importing (extracting product ion data) from only light peptide even though heavy & light are both in RAW file mlane  2019-10-02
Hi, Upon recently updating Skyline Daily version to, targeted MS raw data files (PRM data generated from Orbitrap Lumos) is not fully imported into Skyline documents. We went back to official Skyline release (most current v 19.1) with the same file, created new document and the problem was resolved. Also, on multiple PCs, we created new Skyline Daily version document template, and the problem repeated. The raw files are confidential, but if you need help with source files to recreate the issue, let us know and we will try to come up with a example that is not confidential. At minimum, can you send link or instructions to install previous version of Skyline Daily (we did not have issue in previous release)?
Nick Shulman responded:  2019-10-02
One way to go back to the earlier version of Skyline-Daily is to go to Control Panel Programs and Features. When you click "Uninstall/Change" on Skyline-Daily, you will be asked whether you want to Restore the application to its previous state. That option will take you back to the previous version.

Another thing that you can do is install the "unplugged" build of Skyline-Daily:

I am aware of one problem with chromatogram extraction in the most recent Skyline-Daily. If your MS2 scans have more than one isolation window (we sometimes call this "MSX") then the most recent Skyline-Daily will not extract MS2 chromatograms from them. This will be fixed in the next update of Skyline-Daily. You can read about that bug here:

-- Nick
mlane responded:  2019-10-02
Thank you for the prompt response, Nick! The version installation is very helpful. I just wanted to add that (in our case anyway) we are seeing the issue in files that were generated both with and without MSX enabled. We do tend to multiplex different charge states together (not heavy and light) if our target list is especially long. I'm not sure if our issue is unique to Lumos data, but another property is that we have both full MS and a PRM channels in our method.
Nick Shulman responded:  2019-10-02
I am not sure whether the bug with your data is the same as what we fixed.

One way that you could check whether the future release of Skyline-Daily is going to fix your problem is to check whether the most recent MSConvert fixes it.
You can install the latest version of MSConvert from here:

You can use MSConvert in ProteoWizard to produce a .mzML file. If the current Skyline-Daily does not have a problem with that .mzML, then the next release of Skyline-Daily will work correctly with your .raw file.

I will also send you an email in case you want to discuss your files privately.
-- Nick