a) Electrospray ionization is well known for creating multiply charged analyte ions, e.g., multiply protonated [M+nH]n+ species. Do you expect doubly or triply protonated molecules to be suitable for MS/MS? Will they undergo fragmentation easier than singly charged ions or won’t they work at all?
Charges of equal polarity on the same molecule create Coulombic repulsion. This is why the number of charges per molecule is limited, e.g., in case of peptides it is roughly limited to one charge per 1000 u of molecular mass. Multiple charging thus helps to tear an ion apart provided the charges are located in the opposite parts of the dissociation ion. Therefore, doubly or even triply charged ions undergo fragmentation at lower collision energies than their singly charged counterparts. In proteomics, [M+2H]2+ peptide ions are even preferred as precursor ions.
b) Which method of ion dissociation depends on the presence of multiply charged precursor ions?
Electron capture dissociation (ECD) requires at least doubly charged precursor ions to be selected because one charge becomes neutralized upon electron capture to form a radical ion carrying one charge less than the precursor ion. For example, a [M+5H]5+ precursor will form quickly dissociating [M+5H]4+. upon ECD. While a singly charged precursor ion may undergo ECD, it will only yield neutral fragments that are useless for MS detection.
c) Consider a [M+2H]2+ peptide ion that is subjected to dissociation. Explain which m/z range you are going to scan and why you decided to do so.
Fragmentation of the doubly charged precursor can yield doubly charged as well as singly charged fragment ions depending on where the charge(s) reside with respect to the bond cleaved. Loss of a low-mass ion from such a precursor will thus form a singly charged fragment ion of a mass close to M. Fragment ions may therefore be formed close to an m/z corresponding to singly charged ions of M, .i.e., may appear not only below but also above the m/z of the doubly charged precursor ion. So it is save to scan up to m/z equal to the numerical value of M.