Magnetic microparticles with dedicated, functionalized surfaces are used to bind specific proteins and peptides. After binding the proteins to the magnetic beads, removal of supernatants and washing steps, the purified samples are eluted and transferred onto AnchorChip™ targets for subsequent measurement in the MALDI-TOF mass spectrometer. Magnetic bead sample preparation is facile, scalable and highly reproducible. It can be done manually as well as automated by the ClinProt robot. Sample and protocol information are identified via barcode and transferred to the mass spectrometer via transponder code.