|Consistent protein identifications are the cornerstone for biomarker discovery, verification, and validation studies. Even slight variations in laboratory technique while carrying out steps of a protocol for sample preparation can lead to inconsistent protein identifications from sample to sample. To overcome this inconsistency, we have designed and developed a high-throughput automated system capable of preparing clinical samples for mass spectrometry analysis. This automated platform was designed specifically to process plasma samples using a SISCAPA workflow. The ultimate sample preparation throughput of almost 1,000 samples per day represents, to the best of our knowledge, an unparalleled capability unique to our Center.