ProteinChip

Davies, H., Lomas, L., and Austen, B. (1999). Profiling of amyloid b peptide variants using SELDI ProteinChip arrays. BioTechniques 27, 1258-1261,... 

Wright, G. L., Cazares, L. H., Leung, S.-M., Nasim, S., Adam, B.-L., Yip, T.-T., Schellhammer, P. F., Gong, L., and Vlahou, A. (2000). ProteinChip surface enhanced laser desorption/ionization (SELDI) mass spectrometry a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer and Prostatic Diseases 2, 264-276. 

The ProteinChip System from Ciphergen Biosystems uses patented SELDI (Surface-Enhanced Laser Desorption/Ionization) ProteinChip technology to rapidly perform the separation, detection, and analysis of proteins at the femtomole level directly from biological samples. ProteinChip Systems use ProteinChip Arrays which contain chemically (cationic, anionic, hydrophobic, hydrophilic, etc.) or biochemically (antibody, receptor, DNA, etc.) treated surfaces for specific interaction with proteins of interest. Selected washes create on-chip, high-resolution protein maps. This protein mass profile, or reten-tate map of the proteins bound to each of the ProteinChip Array surfaces, is quantitatively detected in minutes by the ProteinChip Reader. 

Diamond DL, Zhang Y, Gaiger A, et al. Use of ProteinChip array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify thymosin beta-4, a differentially secreted protein from lymphoblastoid cell lines. J. Am. Soc. Mass Spectrom. 2003 14 760-765. 

Ernst G, Melle C, Schimmel B, et al. Proteohistography—direct analysis of tissue with high sensitivity and high spatial resolution using ProteinChip technology. /. Histochem. Cytochem. 2006 54 13-17. 

The protein profiling approach also provides the use of pattern recognition for discrimination of disease states. Biomarkers for prostate cancer were profiled and a panel assembled that could differentiate cancer patients from noncancer populations (see Fung et al., 2001, Reference 11). Poon et al. (2003) utilized the ProteinChip to obtain tumor-specific proteomic signatures to detect hepatocellular carcinoma (HCC) in patients having chronic liver disease (CLD). 

Batorfi, J., Ye, B., Mok, S.C., Cseh, I., Berkowitz, R.S., and Fulop, V., Protein profiling of complete mole and normal placenta using ProteinChip analysis of laser capture microdissected cells, Gynecol. Oncol., 88, 424-428, 2003. 

Melle, C., Ernst, G., Schimmel, B., Bleul, A, Koscielny, S., Wiesner, A., Bogumil, R., Moller, U., Osterloh, D., Halbhuber, K.J., and F. Von Eggling, 2003, Biomarker Discovery and Identification in Laser Microdissected Head and Neck Squamous Cell Carcinoma with ProteinChip(R) Technology, Two-dimensional Gel Electrophoresis, Tandem Mass Spectrometry, and Immunohistochemistry. Mol Cell Proteomics. 2(7) 443-52. 

Shiwa, M., Nishimura, Y., Wakatabe, R., Fukawa, A., Arikuni, H., Ota, H., Kato, Y., and Yamori, T. 2003. Rapid discovery and identification of a tissue-specific tumor biomarker from 39 human cancer cell lines using the SELDI ProteinChip platform. Biochem. Biophys. Res. Commun. 309, 18-25. 

Dayal B, Ertel NH ProteinChip technology a new and facile method for the identification and measurement of high-den-sity lipoproteins apoA-I and apoA-II and their glycosylated products in patients with diabetes and cardiovascular disease. 

Despite its clever utility, SELDI suffers from several limitations. The SELDI MS instrumentation usually is capable of accurately detecting proteins with molecular weights less than 45,000, the detected proteins cannot be identified using this technique alone, and reproducibility in complicated experiments is suspect (86). Improvements in next-generation instruments using ProteinChip tandem MS techniques that enable direct protein identification (87), improved surface chemistries (88), and improved experimental design (89,90) should all greatly enhance SELDI s effectiveness as a powerful proteomic tool (91,92). 

He QY, Yip TT, Li M, Chiu JF. Proteomic analyses of arsenic-induced cell transformation with SELDI-TOF ProteinChip technology. J Cell Biochem 2003 88 1-8. 

Austen BM, Frears ER, Davies H. The use of solid ProteinChip arrays to monitor production of Alzheimer s beta amyloid in transfected cells. J Pept Sci 2000 6 459-469. 

Cordingley HC, Roberts SL, Tooke P, Armitage JR, Lane PW, Wu W, Wildsmith SE. Multifactorial screening design and analysis of SELDI-TOF ProteinChip array optimization experiments. Biotechniques 2003 34 364-365, 368-373. 

Wiesner A. Detection of tumor markers with ProteinChip(R) technology. Curr Pharm Biotechnol 2004 5 45-67. 

Reddy G, Dalmasso EA. SELDI ProteinChip(R) array technology protein-based predictive medicine and drug discovery applications. J Biomed Biotechnol 2003 2003 237-241. 

Key Words Alzheimer s disease A(3 amyloid precursor protein SELDI-TOF MS ProteinChip technology. 

ProteinChip arrays with preactivated surfaces are also available for covalently coupling of a specific bait molecule (protein, DNA, RNA). This allows the investigation of specific protein interactions such as DNA-protein, receptor-ligand, and antibody-antigen (Ab-Ag), the latter of which permits the generation of a standard curve and hence quantitation studies (21). 

In contrast, ProteinChip technology allows the detailed analysis of A(3 fragments and their modifications (22). Peptides are captured on arrays coated with anti-Ap Ab, washed to remove nonspecifically bound fragments, and finally detected by SELDI-TOF MS. The resolution of the technique allows the discrimination of peptides of similar mass and modified products, e.g., oxidized peptides versus native peptides, which differ by only 16 Da. ProteinChip technology has been used extensively to detect Af> fragments in various samples, including cell culture supernatants, serum, plasma, and cerebrospinal fluid (CSF) (21-23). 

Capture and Quantitation of Aft Using Antibody-Coated ProteinChip Arrays... 

The preferred Abs for ProteinChip experiments are Ag affinity purified polyclonal Abs (pAb), they exhibit a high avidity and slow off rate. In addition, Ab must be pure and intact ( 150 kDa), as contaminating proteins or free Ab light/heavy chains ( 25 and 50 kDa, respectively) will compete for active sites on the preactivated array and diminish the specific signal between the intact Ab and Ag (see Note 2). Further to this, it is important to assess the Ab buffer constituents the buffer must be free of amines (Tris, ethanolamine, azide) as this will also compete for the active sites and diminish the specific signal of the Ab/Ag interaction. 

Load 2 il, of anti-A(3 Ab or control Ab (0.1-0.5 mg/mL) to each spot of a preactivated ProteinChip array. As PS 10 and PS20 arrays are commonly used for A(3 capture experiments, analysis of these chip types will be described. 

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