Which tutorial are you referring to?

There are only a couple of ways that you can control the colors of things in Skyline.
One is that if you right-click on anything in the Targets tree, you can set it's "Note". The things in the tree that have a note are indicated by a tiny triangle. When you are setting the Note in the Edit Note dialog, you also have the ability to control the color of that triangle. But that will not affect the color of anything like the chromatograms or the peak areas graph.

The other way to customize colors is by changing the color scheme at:
Tools > Options > Display

I do not know of any feature that sounds like what you are describing but I might have forgotten something.
-- Nick

Hello Nick,

Great to hear from you. Yes, I would like to change the colors of the chromatography for the small molecule peaks. Specifically, I would like one color for the peak I choose so that I can display multiple peaks.

There is a tutorial for this about "how to display multiple peptides", however, I would like to achieve the same effect with small molecules.

Here is an image of what the peptides looks like with different colors for each peak.

Is this possible to do with small molecules? I have a friend who achieve this with other metabolites, but she has since forgotten how she did this and currently neither of us can seem to reproduce it.

Skyline has four levels of things displayed in the Targets tree.
In a proteomic document, those four levels are called "Protein", "Peptide", "Precursor" and "Transition".

In a small molecule document, those levels are called "Molecule List", "Molecule", "Precursor" and "Transition".

In your latest screenshot, Skyline is displaying the chromatograms from multiple peptides because the Protein is selected.
If you wanted a similar graph to be displayed in your document, you would select a Molecule List.
Your document has one Molecule List which is named "Amino Acid", and which is the topmost element displayed in the Targets tree.

You can also select multiple molecules in the Targets tree by shift-clicking (to selecting a continuous range of nodes in the tree), or ctrl-clicking (to add or remove a particular node from the selection).

You can also press Ctrl + A to select everything in the tree.

-- Nick

Hello, apologies for calling up a 4+ year old thread, but I seem to be running a similar issue.

Is there a way to user-define the colors assigned at the "Molecule" level?
It seems that the color is determined based on the first letter/character in the Molecule's name, e.g. "1Bradykinin" vs. "Bradykinin".

I am operating in the "Molecule" mode; even though I'm analyzing peptides, but there are discrete mass additions that I'm monitoring. Thanks.

ehcan27006,

Unfortunately, no, there is still no way to customize the colors that Skyline chooses.

In the screenshot "Brad.jpg", those colors are actually a little different.
The first color is #027868 and the second is #007737.
The first color has more blue in it than the second.

The color that Skyline assigns to a molecule is based on the hash code of the molecule's name. It is a mathematical function that really does look at each character in the molecule's name.
There is also a second step which looks at the colors that have been assigned to all of the other molecules in the same molecule list, and if there are any colors which are too close to each other, then a different color is assigned to that one.

The amount of blue in the two colors in your screenshot is sufficiently different so that Skyline does not think that it needs to pick a different color.

The C Sharp code for this logic is here:
https://github.com/ProteoWizard/pwiz/blob/master/pwiz_tools/Skyline/Model/ColorGenerator.cs

I am not sure whether we have any plans to make this work better, but I agree there is some room for improvement.
-- Nick