Targeting the early oligomerization of amyloid beta protein (A beta) is a promising therapeutic strategy for Alzheimer's disease (AD). Recently, certain C-terminal fragments (CTFs) derived from A beta 42 were shown to be potent inhibitors of A beta-induced toxicity. The shortest peptide studied, A beta(39-42), has been shown to modulate A beta oligomerization and inhibit A beta toxicity. Understanding the mechanism of these CTFs, especially A beta(39-42), is of significance for future therapeutic development of AD and peptidornimetic-based drug development. Here we used ion mobility spectrometry-mass spectrometry to investigate the interactions between two modified A beta(39-42) derivatives, VVIA-NH2 and Ac-VVIA, and full-length A beta 42. VVIA-NH2 was previously shown to inhibit A beta toxicity, whereas Ac-VVIA did not. Our mass spectrometry analysis revealed that VVIA-NH2 binds directly to A beta 42 monomer and small.oligomers while Ac-VVIA binds only to A beta 42 monomer. Ion mobility studies showed that VVIA-NH2 modulates A beta 42 oligomerization by not only inhibiting the dodecamer formation but also disaggregating preformed A beta 42 dodecamer. Ac-VVIA. also inhibits and removes preformed A beta 42 dodecamer. However, the A beta 42 sample with the addition of AcVVIA clogged the nanospray tip easily, indicating that larger aggregates are formed in the solution in the presence of Ac-VVIA. Molecular dynamics simulations suggested that VVIA-NH2 binds specifically to the C-terminal region of A beta 42 while Ac-VVIA. binds dispersedly to multiple regions of A beta 42. This work implies that C-terminal interactions and binding to A beta oligomers are important for C-terminal fragment inhibitors.