Taking peptides (in CHCA matrix) as an example, why would most ions produced carries an 'overall net' +1 charge?
As a peptide must contain different combinations of acidic and basic amino acids (hence side chains are of different charges). How would all these charges add-up / behave (were they shielded?).
I am curious as in most database searches (e.g. Mascot), in essentially all cases, we set the peptide charge parameter to +1 and it works fine every time (i.e. most peaks in the spectrum could be matched in no problem).
Thanks.