The formation of the complexes between Cibacron blue F3G-A and two therapeutic proteins, recombinant human interferon-alpha2b and recombinant human growth hormone, was investigated. The method of time-resolved limited proteolysis coupled with MALDI-TOF mass spectrometry was used. The analysis of peptide maps revealed that A(17)HR(19) and L(20)HQLAFDTYQEFEEAYIPK(38) of hGH, and R(14)TLMLLAQMR(23) and D(33)RHDFGFPQEEFGNQFQK(50) of hIFN-alpha2b, exhibit affinity to Cibacron blue F3G-A.