A method of detecting an antigen in a sample, the method comprising: (a) contacting the sample with a first affinity agent and a second affinity agent, wherein the second affinity agent is linked to a magnetic bead and wherein the first and second affinity agents specifically bind to the antigen, if present, and contacting the sample that had been contacted with the first and second affinity agents with a third affinity agent, wherein the third affinity agent comprises a label and wherein the third affinity agent specifically binds to the first affinity agent, thereby forming an antigen-affinity agent-label complex; or (a') contacting the sample with a first affinity agent and a second affinity agent, wherein the first affinity agent comprises a label, wherein the second affinity agent is linked to a magnetic bead, and wherein the first and second affinity agents specifically bind to the antigen, if present, thereby forming an antigen-affinity agent-label complex; or (a") contacting the sample with the antigen and a first affinity agent, wherein the first affinity agent is linked to a magnetic bead and specifically binds to the antigen, thereby forming an analyte-antigen-affinity agent complex, and contacting the sample comprising the analyte-antigen-affinity agent complex with a second affinity agent, wherein the second affinity agent comprises a label and specifically binds to the antibody analyte, thereby forming an analyte-antigen-affinity agent-label complex; (b) separating the antigen-affinity agent-label complex from uncomplexed components in the sample based on the presence or absence of the magnetic bead, thereby generating a separated sample comprising the antigen-affinity agent-label complex; (c) partitioning at least the label from the separated sample into a plurality of partitions; and (d) detecting the presence of the label in at least one partition; thereby detecting the presence of the antigen. (a) contacting the sample with a first affinity agent and a second affinity agent, wherein the second affinity agent is linked to a magnetic bead and wherein the first and second affinity agents specifically bind to the antigen, if present, and contacting the sample that had been contacted with the first and second affinity agents with a third affinity agent, wherein the third affinity agent comprises a label and wherein the third affinity agent specifically binds to the first affinity agent, thereby forming an antigen-affinity agent-label complex; or (a') contacting the sample with a first affinity agent and a second affinity agent, wherein the first affinity agent comprises a label, wherein the second affinity agent is linked to a magnetic bead, and wherein the first and second affinity agents specifically bind to the antigen, if present, thereby forming an antigen-affinity agent-label complex; or (a") contacting the sample with the antigen and a first affinity agent, wherein the first affinity agent is linked to a magnetic bead and specifically binds to the antigen, thereby forming an analyte-antigen-affinity agent complex, and contacting the sample comprising the analyte-antigen-affinity agent complex with a second affinity agent, wherein the second affinity agent comprises a label and specifically binds to the antibody analyte, thereby forming an analyte-antigen-affinity agent-label complex; (b) separating the antigen-affinity agent-label complex from uncomplexed components in the sample based on the presence or absence of the magnetic bead, thereby generating a separated sample comprising the antigen-affinity agent-label complex; (c) partitioning at least the label from the separated sample into a plurality of partitions; and (d) detecting the presence of the label in at least one partition; thereby detecting the presence of the antigen.