Methods of identifying ligand binding sites in a target molecule such as a
polynucleotide or polypeptide, as well as methods for determining whether
a particular site in a target molecule is at or near the ligand binding
site, are provided. Ligand binding affinities corresponding to both the
target molecule and a modified version thereof are compared, preferably
using mass spectral analysis. The modified molecules, or test molecules,
incorporate a modification capable of modulating ligand binding affinity
when located at or near the ligand binding sites. Binding site information
is derived from the known position of the modification.
