ammonium salts are added to replace some of the sodium bound to the
DNA/RNA. If we omit ammonium salts we do not get signals at all or we
measure only higher order adducts of sodium to the DNA/RNA. If sodium
adducts become a bigger problem you might want to consider additional
desalting of the sample prior to the addition of matrix.
Best wishes,
Juri Rappsilber
Protein Interaction Laboratory
University of Southern Denmark