We herein describe an analytical method employing a small molecule array for the characterization of similar proteins based on ligand binding. In this study, 2 different beta amyloids (Abeta(1-40) and (1-42)) were selected as the model compounds. Their primary structures are identical except for 2 additional C-terminal amino acids. However, many studies have observed different biological and chemical characteristics of these peptides. Thus, the ability to distinguish these 2 peptides is important in the diagnosis and development of treatments for related disorders such as Alzheimer's disease. However, strong non-specific binding is usually observed, even when specific antibodies for each peptide are employed. In this study, Abeta(1-40) and Abeta(1-42) peptides were immobilized on a typical 96-well microplate. Twenty different small probe molecules (modified amino acids conjugated with FITC) were applied to the peptides acting as the secondary antibodies and labeling compounds. The results show that specific binding patterns occurred according to Abeta type and the analysis of the patterns can be used to distinguish these 2 similar peptides.