Small Molecule Precursor Name Waters Data error? viragsagikiss  2021-10-07

Hi all,

Apologies if this questions has been already answered, but I cannot find an answer.

Some of the analytes will not be displayed in Skyline no matter how hard I try to match with the Precursor Name with the Precursor Name I used when creating it in Masslynx.
I took great care to match capitals, spaces, dots, hyphens and so on, but mysteriously some Precursor Name I can rename to anything and will work, while with other Precursor Name even a space difference in the Precursor Name will make it "vanish". IT doesn't seem to correlate with the "complexity" of the Precursor name as you see on the screenshot, hexoseamine (misspelled originally...) is a simple name while other more elaborated naming works just fine.
I hope this question makes sense, attached a screenshot of the problem.

Any idea?

Thank you!

Best regards,

Skyline: daily
Waters TQ-S with latest Masslynx Software

Nick Shulman responded:  2021-10-07
I am not sure that I understand your question, but if you send us your Skyline document we might be able to figure it out.
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:

It sounds like you are saying that you are clicking somewhere in Skyline and renaming a precursor, and the precursor is disappearing. Can you give us more detail about what exactly you are doing?

When you change the name of a molecule in Skyline, it will often lose its chromatogram data if you have already extracted chromatograms for it. This is because the chromatograms are stored in the .skyd file, and the name is usually part of how Skyline figures out which chromatogram in the .skyd file belongs to which molecule in the document. If you rename any of your molecules you should usually tell Skyline to extract chromatograms again by going to:
Edit > Manage Results > Reimport

If your question has to do with chromatograms disappearing, you should send us one of your raw files in addition to your
-- Nick
viragsagikiss responded:  2021-10-08
Hi Nick,

Thanks for the quick answer.

Your answer solved my problem, as reimporting the data helped.
Just to clarify, my problem was not renaming but that I could not "read in" data for certain small molecules and i could not figure out why, now i realised it is related to the exact retention times were out of the MRM RT window set. But that didn't occur to me earlier as changing exact RT did not solve the problem without reimporting the result files.

Thank you!