Can you send us your Skyline document?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing the Skyline document and supporting files.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url

After we see your Skyline document we will probably be able to tell you what is going on.
The Transition Settings control which transitions Skyline gives you by default.
You can right-click on things in the Targets tree and choose "Pick Children" to add other things that Skyline has not given you.
You might need to toggle the Filter button in the child picker window in order to see the options that you want.
--Nick

Sure, thanks! I have attached the file. The precursor I am working with is 936.8028+++

Best,
Chelsea

Unfortunately, that's the wrong file.
Can you attach a .sky.zip file that you create using the "File > Share" menu item?
-- Nick

Sorry about that, hopefully this is correct.

Best,
Chelsea

I'm unable to attach the zip file to the support request because it is too large and I'm unable to upload it to the link you provided (the upload crashes every time). Do you have another way for me to provide the files you need?

Best,
Chelsea

Thank you for uploading that Skyline document.

Skyline is using the settings on the "Filter" tab at "Settings > Transition Settings" to decide which transitions to give you by default.

You can always add more transitions by right-clicking on a Precursor node in the Targets tree and choosing "Pick Children". The Precursor nodes are the ones that say "idotp".
For everything in the Targets tree, Skyline remembers if you have made a change to the set of children that the node has, or whether Skyline is managing that node's children.
When you make changes to Transition Filter settings, that will only affect the nodes for whom Skyline is still managing the children.
When you bring up the child picker window using the "Pick Children" menu item, there is a magic wand button which controls whether Skyline is managing the children.

The settings that you have on the "Filter" tab at "Settings > Transition Settings" are unusual.
In the "Ion Types" box you have "b, p".
Usually, "y" ions are much more important than "b" ions. This has something to do with the way that lysine ionizes and the mass spectrometer fragments things.
-- Nick

Hi Nick,

Thanks for your suggestion. I tried using the pick children option but it only included b-ions >b10 and I would be interested in seeing b9, b8, b7, etc... do you have any suggestions for how I could include more b-ions below b10? I included a screenshot of what I am referring to in the "pick children" menu that came up.

As for my strange settings - for my purposes, I'm only interested in the b-ions so I didn't include y-ions at all.

Best,
Chelsea

In the "Product ion selection" on the "Filter" tab at "Settings > Transition Settings", the "From:" selection is "m/z > precursor" which means that, by default, Skyline will only give you transitions whose m/z is greater than the m/z of their precursor.
If you want Skyline to give you more ions than that, you could change that setting to something else like "ion 1" if you want to include all of the ions including "b1".

Alternatively, in the Child Picker window in your screenshot, you could click the filter button so that Skyline will allow you to choose transitions that do not satisfy the filter criteria. The filter button is the third button down on the left side of your screenshot.
-- Nick

That fixed it! Thanks so much Nick!

Best,
Chelsea