Mass spectrometric ITEM-ONE analysis confirms and refines an assembled affimer binding site on the HER-2 targeting therapeutic antibody Pertuzumab

The Pertuzumab-binding affimer 00557_709097 was incubated either with peptides from tryptically digested Pertuzumab or with selected synthesized peptides. Affimer-peptide complexes were subjected to nano electrospray mass spectrometric ITEM analyses in order to identify the affimer’s epitope on Pertuzumab. Furthermore the affimer was incubated with intact Pertuzmab to determine apparent binding energies and dissociation constants of the complex dissociation reactions in the gas phase using ITEM-TWO.