Centrifugally-enhanced method of determining ligand/target affinity

A method of selecting one or more compounds which demonstrate affinity binding to a pre-selected target substance comprising the steps of:

• a) exposing at least one target substance to a mixture of compounds in a a container vessel;
• b) subjecting the container vessel and contents to centrifugation;
• c) collecting a data array of full scale mass spectral scans of signal intensities for each of several samples collected from the contents of the container vessel at successively greater depths of the container vessel;
• d) displaying the data array as a 3-dimensional plot in which one axis represents m/z, the second axis represents depth in the container vessel, and the third axis represents mass spectral signal intensity;
• and
• e) viewing the 3-dimensional plot at one or more planar cuts taken at one or more constant values of m/z in the 3-dimensional plot to select one or more compounds

A method of determining, in a protein known to bind to a pre-selected target substance, a specific region of the protein required for binding to the target substance, the method comprising the steps of:

• a) preparing a fragment of the protein tagged at one terminus with a marker, and having a pre-determined number of aminoacyl residues deleted from the opposite terminus;
• b) exposing the tagged protein fragment to the pre-selected target substance in a a container vessel;
• c) subjecting the container vessel and contents to centrifugation;
• d) determining the concentration gradient of tagged protein in the container vessel by an analytical technique sensitive to the detectable marker;
• e) iterating steps a) through d) on successively shorter fragments of the protein until the concentration gradient data indicate the absence of binding between the protein fragment and the pre-selected target substance.