(This tip applies to Skyline-Daily 188.8.131.5257 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".
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 "]".
Singly protonated: [M+H]
Doubly deprotonated: [M-2H]
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]
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:
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+]