Immunoproteomics allows the detection and characterization of multiple types of analytes (such as antigens and antibodies) from different sources of body fluids and tissue/cell lysates in healthy and diseased subjects. FLEXMAP 3D is a recent platform, which applies immunoproteomics as a main approach. It was previously used to profile and detect various types of analytes in a timely manner with high levels of accuracy, sensitivity, and specificity. In this chapter, a simplified protocol is stated of how we can characterize general human antibody profiles against pathogens using FLEXMAP 3D. In this experiment, we have looked for antibody response against 6 different bacterial/fungal supernatants in 16 patients’ plasma (comparing 8 type 2 diabetes patients with 8 healthy people).