SELDI protein chips

Boyle et al. (2001) used the Ciphergen SELDI protein chip to analyze the secretion and autoactivation of a cysteine protease (SpeB) from Streptococcus pyogenes that has been implicated in the onset of group A streptococcal infections and may contribute to toxic shock symptoms. SpeB could be detected at 0.75 ng protein in a 30-min assay based upon SELDI-TOF... 

Davies, H., Lomas, L., and Austen, B. (1999) Profiling of amyloid beta-peptide variants using SELDI protein chip arrays. Biotechniques 27 1258-1261. 

FIGURE 7 Group B streptococcus infection-induced differential protein expression in nonhuman primate (A) and human (B) amniotic fluid samples by surface-enhanced laser desorption/ionization (SELDI-TOF MS) using normal-phase protein chip arrays. Spectrum from 2.5 to 15 kDa collected at 235 nm laser intensity. Detailed spectra show increased expression of the 3.5 and 10.8 kDa peaks between control and infected. Arrows indicate the unique peaks represented by polypeptides overexpressed in infection. 

SELDI-TOF is beginning to offer an alternative to 2DGE. Surface-enhanced laser desorption/ionizitation (SELDI) is an affinity-based mass spectrometric method in which proteins of interest are selectively adsorbed to a chemically modified surface on a biochip (Ciphergen Protein Chip Arrays). 

Protein Chip technology, it will be possible to simultaneously analyze protein profiles of body fluids such as serum and urine samples very rapidly. The SELDI mass spectrometry in conjunction with bioinformatics tools could greatly facilitate the discovery of new and improved toxicologic biomarkers. 

Surface-enhanced laser/desorption ionization mass spectrometry Protein-Chip . See Tang, N., Tomatore, P, and Weinberger, S.R., Current developments in SELDI affinity technology. Mass Spectrom. Rev. 23a, 34-44,2004. 

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. 

Surface enhanced laser desorption ionisation (SELDI) is a version of MALDI with the addition of a special chip from which sample components are ionised and desorbed. The chip can be a protein chip array composed of spots of different chromatographic surfaces (which are chemical or biochemical in nature) designed to retain specific proteins. Its main advantage is inclusion of this separation/selection step for crude or complex samples prior to MS analysis. 

Two methods are used to capture proteomes 2D electrophoresis (Section 7.3) and the SELDI protein chip system (Section 7.5). These methods are complemented by the good old micro-sequencing (Section 7.6) and different mass spectroscopic methods (Sections 7.4 and 7.6.5). After all, via partial sequences and the exact MW the proteins of a spectrum can be unambiguously identified in databases. 

The almost endless possibilities of mass spectrometry have been increased by yet another hopeful variant SELDI (surface-enhanced laser desorption ionization). SELDI combines protein chips with a UV-MALDl-TOF. The chips are solid aluminum strips coated with cationic or anionic ion exchangers, with hydrophile or hydrophobic molecules. Chips with activated surfaces are also available. These bind proteins covalently via their amino groups and enable you to coat chips with antibodies or receptors as you need them. Every chip has eight coated holes with a diameter of 1 mm. You apply the sample into the holes. Part of the pro-teins/peptides is adsorbed. The remainder is washed off. The adsorbed proteins/peptides are transferred into matrix and can then be analyzed in the mass spectrometer (Figure 7.8). What can SELDI do better than MALDI ... 

Surface-enhanced laser desorption ionization (SELDI) uses so-called protein chips for the detection of peptides and proteins from complex biological fluids such as blood or urine, often for the identification of diagnostic biomarkers for specific carcinomas [156, 157]. These protein chips can contain various media for positive or negative ion exchange or reverse-phase chromatography, as well as specific antibodies or DNA. The functionaUzed surface is immobihzed on a MALDl sample plate for the selective enrichment of constituents of the complex mixture applied, whereas the not bound supernatant is removed by washing. Unfortunately, a large number of unsubstantiated claims for the detection of disease-related biomarkers has discredited this approach, mostly as a result of poor mass spectrometric performance. 

In 1993, Hutchens and co-workers described surface-enhanced laser desorption/ionization (SELDI) technique, an affinity technology, which has progressed over the last decade to become a powerful analytical, an on-plate approach (Hutchens and Yip 1993). SELDI is a distinctive form of laser desorption/ionization (LDI) mass spectrometry in which the EDI probe plays an active role in the homogenization, preconcentration, amplification, purification, extraction, enrichment digestion, derivatization, synthesis, separation, and detection with complementary techniques, prior to the desorption and ionization of the analytes by MALDI (Merchant and Weinberger 2000). The principle of this approach is very simple. Biomolecules are captured by adsorption, partition, electrostatic interaction, or affinity chromatography on a solid-phase protein chip surface. Although SELDI provides a unique sample preparation platform, it is similar to MALDI-MS in that a laser... 

SELDI-MS based on protein-chip arrays have been utilized for the selective and rapid identifieation of S. aureus from other non S. aureus species (Yang et al. 2009). Fiuthermore, the protein chips have also been employed for the rapid identification of antibiotic resistance ofE. coli (Dubska et al. 2011). 

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. 

Matrix-assisted laser desorption ionization (MALDI) and surface-enhanced laser desorption ionization (SELDI) have been used online with TOF-MS for protein differential profiles of intact or hydrolyzed biological matrices in proteomics. The potential use of affinity chips, grafted with specific Ab towards the drug compound for MALDI or SELDI, will bring sensitive and selective tools for macromolecules. Specific Ab towards either the intact protein or several signature peptides... 

Figure 6 The SELDI technology. This type of proteomic analytical tool is a class of mass spectroscopy instrument that is useful in high-throughput proteomic fingerprinting of serum. Using a robotic sample dispenser, 1 p,L of serum is applied to the surface of a protein-binding chip. A subset of the proteins in the sample binds to the surface of the chip. The bound proteins are treated with a matrix-assisted laser desorption and ionization matrix and are washed and dried. The chip, which contains multiple patient samples, is inserted into a vacuum chamber where it is irradiated with a laser. The laser desorbs the adherent proteins and causes them to be launched as ions. The TOF of the ion before detection by an electrode is a measure of the mass-to-charge (m/z) value of the ion. The ion spectra can be analyzed by computer-assisted tools that classify a subset of the spectra by characteristic patterns of relative intensity (adapted from www.evmsdoctors.com).

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