In accordance with an embodiment of the invention, there is provided a method for: a) high-throughput, multiplexed, affinity-based separation of proteins—especially low abundance proteins—from complex biological mixtures such as serum; and b) high-throughput, multiplexed, affinity-based separation of cells—especially rare cells—from complex biological mixtures such as blood or blood fractions. The separation of proteins or cells is achieved based on differential binding to affinity-capture beads of different sizes and then sorting the protein-bound or cell-bound beads using the concept of centrifugal-induced Dean migration in a spiral microfluidic device. This method enables continuous-flow, high throughput affinity-separation of milligram-scale protein samples or millions of cells in minutes after binding. This is particularly applicable to the isolation of antigen-specific antibodies from polyclonal sera and antigen-specific immune cells or circulating tumor cells from blood, both of which are otherwise highly labor-intensive and expensive to perform.