Overview of the SELDI System

Current studies of the BDL are focused on applying Ciphergen Biosystems SELDI-TOF-MS ProteinChip® system for biomarker discovery of tumor-associated proteins; and as a potential clinical diagnostic assay. Briefly, the SELDI systems in the BDL are PBS-II mass readers with ProteinChip Software and personal computers to analyze proteins captured on the proprietary ProteinChip Arrays.

Figure 1A: SELDI ProteinChip® System Mass reader with computer workstation

Figure 2A: Five surface types of 8 array ProteinChips®

Figure 1C: Beckman/Coulter Biomek 2000® robotic workstation


Figure 1D: SELDI ProteinChip® Process

The Protein Chip Arrays distinguish this technology from other mass spectrometry-based systems. The Arrays provide a variety of surface chemistries for researchers to optimize protein capture and analysis. The chemistries include classical chromatographic surfaces such as hydrophobic for reversed-phase capture, cation-and anion exchange surfaced, immobilized metal affinity capture (IMAC) for capturing metal-binding proteins, and pre-activated surfaces to investigate antibody-antigen, DNA-protein, receptor-ligand, etc.

A typical SELDI experiment is illustrated in FIGURE 2 (below). Chip processing — i.e., adding the protein sample, washing, adding the energy adsorbing molecule (EAM) — can either be done manually or by using a robotic workstation, such as the Biomek 2000 (Beckman/Coulter). The latter becomes essential when analyzing a large number of samples to maximize reproducibility. The chips are then processed in the mass reader where the bound proteins are liberated by ionization, and fly through a "time-of-flight" tube where they separate based on mass and charge.
Figure 2: Illustration of the ProteinChip® SELDI mass spectrometry system

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the full illustration.

The ProteinChip Software then converts the TOF data to generate a mass spectrum profile. The two useful formats (FIGURE 3) for viewing the data are the raw spectrum and the grey-scale (the latter represents a stained one-dimensional electrophoresis gel, hence the name "gel-view").
Figure 3: Representative “raw” spectra and “gel-view” (grey-scale) of serum from a normal donor, and from patients with either BPH (benign prostate hyperplasia) or prostate cancer (PCA) using the IMAC3-Cu chip chemistry

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the full illustration.

For more information about the SELDI profiling studies at the VPC, please contact: