ProteinChip Reader

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. 

Fig. 2. Capture of A(3 using Ab-coated ProteinChip arrays. Preactivated arrays with exposed active sites are shown in (A). Ab are covalently bound to the array via amine groups (B). Exposed active sites are blocked using Tris-containing buffer (C). Samples are added to the array, incubated for 1 1 h (D), and washed to remove nonspecifically bound proteins (E). EAM is applied to each spot (F), and the array is introduced into the ProteinChip reader where the laser is fired onto the chip surface. Proteins retained on the array surface are subsequently resolved via TOF-MS, which displays the mass-to-charge value and signal intensities of each protein (G, H). (Adapted from ProteinChip technology training course, Bio-Rad Laboratories.)...

Typically, for Expression Difference Mapping experiments, chromatographic surfaces are used. The sample requirement is low (1-10 pg total protein per spot), and the sample volume can be freely chosen from 0.5 pL up to around 300 pL. After a short incubation period, unbound proteins and any contaminants on the spot surface are washed away. A solution of energy-absorbing molecules is applied to each of the spots, and the ProteinChip Array is ready for the analysis in the ProteinChip Reader, a highly sensitive laser desorption/ioniza-tion TOF-MS instrament. The results are initially visualized in a graph, with the mass... 

Fig. 8.2 Sample analysis in the ProteinChip Reader. After loading the ProteinChip Array into the ProteinChip Reader, a laser beam is directed onto the sample on the spot. Thereby protons are transferred onto the peptides and proteins that are subsequently accelerated by electromagnetic fields through a flight tube. The time-of-flight is...

ProteinChip Arrays are then analyzed in the ProteinChip Reader, a time-of-flight mass spectrometer. The mass values and signal intensities for the detected proteins and peptides can be viewed in several formats and then transferred to Ciphergen s software suites for further in-depth analysis. 

The ProteinChip System Series 4000 Enterprise AutoBiomarker Edition, comprised a ProteinChip Reader with autoloader capacity to automatically run - simultaneously - up to 168 bar-code-labeled ProteinChip Arrays with, in total, 1344 samples, a customized Biomek 2000 hquid handling robot and CiphergenExpress Data Manager Software for automated sample tracking and advanced data analysis together with the Biomarker Patterns Software for the direct develop-... 

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