Methods for characterizing immune diseases are provided which include exposing a sample of biological fluid from a patient to a pooled population of particles, wherein a first subset of particles is bound to a reactant that binds an antibody and a second subset of particles is bound to a reactant that binds an antigen. The methods further include determining a ratio of measured amounts of the antibody and the antigen in the sample. In some cases, the ratio is compared to one or more standard ratios representing differing states of the disease to determine a state of the disease within the patient. In other embodiments, the steps of exposing and determining a ratio of antibody to antigen are repeated for one or more additional samples of biological fluid taken from the patient. In such cases, at least two ratios are compared to analyze a progression of the disease.