Skyline can automatically add [M+1], [M+2], etc isotopes to your Targets tree if you provide molecular formulas in your transition lists. Here are some things to know about that.

When you first import a transition list, Skyline will only show the most abundant isotope for precursors in the Targets window.

If you want to see others, there are a few settings that need to be adjusted in Transition Settings (via the Skyline Settings > Transition Settings... menu):

• In the Filter tab, make sure the Ion types field includes the letter 'p' to indicate that you want to work with precursors.
• In the Instrument tab, make sure the Min m/z and Max m/z values are suitable for the precursor m/z values you are interested in.
• In the Full Scan tab, make sure the Isotope Peaks value is set to something other than None.

Note: in Skyline versions 21.2 and earlier, even if you have these values preserved in your settings from a previous run you may have to visit the Transition Settings and make a slight change to your settings to provoke the creation of the additional precursor nodes in the Targets window. It doesn't matter which setting, and you can change it back again afterward, but this is necessary to reevaluate the contents of the Targets tree.

Skyline was built from the ground up as a proteomics targeted mass spec research tool. By popular demand, Skyline’s support for more general biomolecular mass spectrometry research has steadily increased over the past several years.

Unfortunately until the Skyline 19.1 release the user interface remained proteomics-centric. Non-proteomics researchers had to think “molecule” while seeing “peptide”, and it wasn’t always easy knowing which parts of the UI didn’t apply to your work. This was especially true for new users.

But now, Skyline adjusts its user interface according to the kind of molecules you're working with.

For full details continue reading the attached PDF.

(This tip applies to Skyline-Daily 3.7.1.11357 and later)

Ionization in Peptides vs Ionization in Small Molecules

Skyline assumes protonation for peptides so we can simply speak about "charge" or "charge states". For generalized molecules, we have to think about all kinds of ionization so we speak in terms of "adducts". Adduct descriptions may also specify isotope labels applied to the neutral molecule description. As such, "adducts" are similar to the idea of "modifications" in the peptide regime. 

Describing Ionizing Adducts

Skyline uses the defacto standard notation for ionizing adduct descriptions, as found at the Fiehn Lab's MS Adduct Caclulator and the GNPS Spectral Library. This notation has a few major parts:

Usually beginning with a left brace "[",

then an optional  dimer/trimer/etc specification,

then an "M"

then an optional isotope label specification,

then the chemical formula of the adduct,

then a closing right brace "]".

Describing Labeled Versions of Molecules for Quantification

For quantification of heavy/light pairs, Skyline expects to see a single molecule with heavy and light adduct descriptions. For example you might describe the light ion as having adduct [M+2H] and its heavy counterpart as having adduct [M4D+2H] (double protonated, and four H replaced by D). Here is a transition list describing that scenario:

Molecule,Precursor Formula,Precursor Adduct
Caffeine,C8H10N4O2,[M+H]
Caffeine,C8H10N4O2,[M4D+H]

The important point is that it describes a common molecule with distinct adduct descriptions, one of which includes labeling information.

Simple Examples

Singly protonated: [M+H]

Doubly deprotonated: [M-2H]

Sodiated: [M+Na]

N-Mer Examples:

Sodiated dimer: [2M+Na]

Deprotonated trimer: [3M-H]

Isotopic Label Examples

Sodiated, and two carbons per molecule replaced with C13: [M2C13+Na]

Sodiated, and two carbons per molecule replaced with C13, and three nitrogens replaced with N15: [M2C133N15+Na]

Charge-Only Examples:

Often transition lists are presented as m/z values with integer charges only, and the actual mode of ionization can not be inferred. In these cases we just give an integer charge value.

Unknown ionization mode, charge = 1: [M+] or [M+1]

Unknown ionization mode, charge = -2: [M-2]

Charge-Only Examples with Isotope Labels Described Only by Mass:

Sometimes a transition list indicated different precursor m/z values for the same named molecule, Skyline reads this as an isotope label of unknown formula, and expresses the mass shift as a number.

Unknown ionization mode, charge = 1, and mass shift due to unknown isotopes of total mass 5: [M5.0+]