Abstract: The present disclosure relates to methods of characterizing protein-protein interaction or conducting immunoassays in a biological sample using self-assembled monolayers (SAMs) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (SAMDI). The biological sample may be obtained from a living subject, such as a human or animal clinical sample containing multiple unknown proteins and/or antigens. Label-free methods of identifying protein-protein interactions, antigen-antibody binding and/or diagnosing a medical condition based on analysis of a biological sample using SAMDI are also provided, as well as biochips comprising surface bound proteins and/or antibodies and methods of making these biochips.