Proteomic approaches to profiling the humoral immune response and identifying disease-associated antigens

In many diseases (e.g. autoimmune diseases, cancer), a humoral immune response is thought to be involved; therefore, identifying relevant antigens that trigger the humoral immune response is at the heart of current approaches for discovering biomarkers and designing therapeutic strategies. Although immunoblotting and protein array have been used for antigen profiling in several diseases, with the rapid progress in mass spectrometry (MS) and separation technologies, MS-based proteomic methods have become a promising tool for identifying disease-associated antigens. This review introduces MS-based antigen profiling methods (immunoproteomics and immune complexome analysis) and presents application examples of these techniques to the analysis of biological samples.