Proteins are the main actors in all physiological and pathological processes. Since the final structure of the protein does not depend on the DNA sequence or even the mRNA sequence alone, the search for direct approaches on the proteome has gained great interest. The most complex and probably the largest proteome is serum, making it clinically the most important. ProteinChip technology, in combination with modern mass spectrometry, allows the complex search for biomarkers, molecular interactions, signaling pathways, and the identification of novel therapeutic compounds. Here we describe the surface-enhanced laser desorption-ionization (SELDI) in combination with the time-of-flight (TOF) mass spectrometry for analyzing serum samples (SELDI was a patented technique from Ciphergen, Fremont, CA). Aluminum-based arrays contain chemical or biological surfaces allowing the capture of proteins, which interact with the surface. The bound proteins are laser desorbed and ionized for mass spectroscopy analysis. The differential mass spectral patterns reflect the protein expression bound on the chip surface and allow the comparison between various samples. Proteins of interest can be identified using peptide mass fingerprinting (PME).