SELDI ProteinChip

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

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. 

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

Wright GL, Jr. SELDI proteinchip MS A platform for biomarker discovery and cancer diagnosis. Expert Rev Mol Diagn 2002 2(6) 549-563. Review. 

Heike Y, Hosokawa M, Osumi S, Fujii D, Aogi K, Takigawa N, et al. Identification of serum proteins related to adverse effects induced by docetaxel infusion from protein expression profiles of serum using SELDI ProteinChip system. Anticancer Res 2005 25(2B) 1197-1203. 

The use of seldi proteinchip arrays to monitor production of Alzheimer s betaamyloid in transfected cells. J. Pept. Sci. 6, 459-469. 

The use of SELDI ProteinChip array technology in 29. renal disease research. Methods Mol. Med. 2003, 86,... 

The SELDI ProteinChip approach allows for high-throughput protein analysis of crude protein mixtures without the need for a separation step. It is sensitive since it takes advantage of the analytical capacity of MS combined with novel surface chemistry. It can provide a phenotypic fingerprint of complex mixtures. Sample requirements are dramatically reduced, and because this approach employs MS... 

One aspect of viral proteomics that is of interest to physicians is the analysis of serum for protein biomarkers of disease. Studies have been performed on patients infected with SAKS-CoV, HIV, HCV, HBV, and HIV-1 using a variety of approaches. Some of the methods that have been used are 2D-PAGE followed by MS, LC/MS/MS, SELDI ProteinChips, and protein microarrays. These methods have their advantages and disadvantages. 2D gel electrophoresis allows for resolution of greater than 1000 protein species, can be used for quantitative analysis of expression, and reflects changes in PTM and the identification of isoforms. However, several issues with 2D gel electrophoresis are its lack of reproducibility, the difficulty in detecting hydrophobic proteins, low sensitivity, and the inability... 

Heike, Y., Hosokawa, M., Osumi, S., Fujii, D., Aogi, K., Takigawa, N., Ida, M., Tajiri, H., Eguchi, K., Shiwa, M., Wakatabe, R., Arikuni, H., Takaue, Y. and Takashima, S., Identification of serum proteins related to adverse effects induced by docetaxel infusion from protein expression profiles of serum using SELDI ProteinChip system. Anticancer Res., 25(2B), 1197-1203 (2005). 

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. 

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. 

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. 

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

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). 

The most popular MS instrument to perform SELDI-TOF MS analysis is the PBS-II, manufactured by Ciphergen Biosystems Inc. [16], The SELDI-TOF MS instrument is composed of three major components the ProteinChip arrays, the mass analyzer, and the data-analysis software. 

FIGURE 4.4 Schematic diagram of the SELDI Ciphergen mass spectrometer. After sample preparation, the ProteinChip arrays are analyzed by a laser-desorption/ionization (LDI) time-of-flight mass spectrometer (TOF MS). The TOF MS measures the molecular weights of the various proteins that are retained on the array. For comparison purposes, the software associated with the SELDI Ciphergen instrument is capable of displaying the resultant data as either a spectral, map, or gel view. 

FIGURE 4.5 Representative spectrum examples of SELDI analysis of pancreatic juice samples bound to IMAC-3 cupper ProteinChip array. A peak of 16,570 Da (arrow) was present in the four pancreatic juice samples from patients with pancreatic adenocarcinoma (PC4, PCS, PC 18, PC24) but absent in the four patients with other pancreatic diseases (IPMN islet cell tumor (ICT) serous cystadenoma (SC)). (Reprinted from Rosty et al. [26], used with permission from the American Association of Cancer Research.)... 

Two hundred and forty-eight serum samples provided from the National Ovarian Cancer Early Detection Program clinic at Northwestern University Hospital (Chicago, IlUnios) were analyzed on the same ProteinChip arrays using both a PBS-II and a Qq-TOF MS fitted with a SELDI interface. The proteomic patterns of the serum samples were acquired on the PBS-II TOF MS, immediately followed by their acquisition on the Qq-TOF MS. The key to this study is that the identical set of serum samples was analyzed on the exact same protein-chip surface, eliminating all experimental variability other than the use of two different instruments. 

Wright, G.L. Cazares, L.H. Leung, S.M. et al. 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 Dis., 2, 264-276 (2000). 

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