This dataset describes the use of biotin-tagged scFv and streptavidin coated magnetic beads for targeted protein captures in the immunoaffinity SRM platform AFFIRM. Proteins are captured using two setups, either incubating scFv and protein in-solution and after binding adding magnetic beads, or by incubating bead-coupled scFv in solution with target protein. Proteins are digested on-bead and analyzed with a peptide SRM readout. Dilution curves of target proteins in serum background from 1-125 ng/ml concentrations are analyzed.