Qualification and calibration kits for use on the Bio-Rad Laboratories’ (Hercules, CA) ProteinChip surface-enhanced laser desorption/ionization (SELDI) system, improve reproducibility during biomarker discovery. Researchers who own either a ProteinChip SELDI Enterprise system or ProteinChip SELDI Personal System can improve long-term reproducibility by qualifying their systems relative to standard specifications. In addition, with the kits, users are able to perform calibrations to compensate for the natural aging of detectors. The tests require no sample preparation or matrix addition. The ProteinChip OQ (operational qualification) Kit includes tests to evaluate nine operational specifications for sensitivity, resolution, and mass accuracy. The ProteinChip System Check Kit verifies reader compliance to four operational specifications for sensitivity and resolution. The ProteinChip Detector Calibration Kit performs detector calibration to automatically adjust detector voltage, thereby optimizing reproducibility over time.