Methods of performing sandwich assays in droplets are disclosed. Further disclosed are methods for detecting a target analyte that involve forming a compartmentalized portion of fluid including a portion of a sample suspected of containing a target analyte and a sample identifier, a first binding agent having a target identifier, and a second binding agent specific to the target analyte under conditions that produce a complex of the first and second binding agents with the target analyte; separating the complexes, and detecting the complexes, thereby detecting the target analyte.