Can you send us what you have ended up with?

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

You can upload that .zip file here:
https://skyline.ms/files.url

We could certainly try going through the tutorial steps again and make sure that they still work, but it might be easier to look at what you have and try to figure out what might have gone wrong.

Just a note that we have an automated test the runs the small molecule tutorial scenario many times on every change. It is still passing. So, yes, we will need your help to understand what went wrong in your particular case.

Thanks for reporting it and working with us to understand the problem.

--Brendan

Thanks, I am bummed to hear that the automated tests do not validate the problems I'm facing. I just uploaded the zip file of my current experiment.

It looks like the links from our website to the tutorial are out of date.
The tutorial files that we meant to have up there should have "3_6" in its name, but all of our links were pointing to the "3_1" version of the tutorial.
I believe something changed in Skyline related to adducts, so if you follow the older version of the tutorial, all of your molecules end up having an extra hydrogen in them.

This is a link to what I believe is the correct version of the tutorial:
https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/SmallMolecule-3_6.pdf
and that tutorial tells you to download this .zip file:
https://skyline.gs.washington.edu/tutorials/SmallMolecule_3_6.zip

The old tutorial, for instance, said that Methionine was "C5H12NO2S", whereas the 3_6 tutorial says "C5H11NO2S".

My assertion that we were running and passing our tutorial tests many times each night and on every commit was intended to give you confidence there might be a simple explanation and a set of tutorial steps that should still work just fine, not to bum you out.

Glad there was indeed a simple explanation, if you were using old "ion-based" (+H as Nick described) chemical formulae, then that would explain why your target transitions didn't match up with the data.

Thanks for pointing this out! We have updated the link. This should save others the pain you unfortunately encountered. Sorry for the inconvenience.

--Brendan

Thanks guys, it has been helpful and the chromatogram showed up and I was able to complete the tutorial.



One point that I think should be changed in the written portion of the tutorial,
"Adduct descriptions can also be used to indicate that a molecule is isotopically labeled. For example, the
adduct “[M3Cl374H2-Na]” indicates that the molecule has three Cl atoms replaced by 37Cl, and two H
atoms replaced by deuterium, and the molecule is ionized by loss of Na."

I think the
two H atoms replaced

should be changed to

four H atoms replaced


Thanks!
Louis Pascal Riel

Hi Louis,

You are quite correct, thank you for catching that!

Brian Pratt