Proteomics Specialized Equipment and Capability

NEW CIPHERGEN ProteinChip Series4000 System

The Proteomic Core of COBRE CCRD is pleased to announce the acquisition of the new ProteinChip Series4000 System. This system will allow the Proteomics Core to greatly facilitate biomarker discovery by taking advantage of important advances Ciphergen has made, namely: increased sensitivity; extended molecular weight range; higher resolution; and the robust statistical analysis capabilities of the CiphergenExpress Biomarker Analysis Module. The multifunctional Series 4000 provides a complete solution for biomarker discovery as well as biomarker interaction analysis and assay development. This type of translational research is of critical importance to COBRE CCRD and is a major objective of the NIH Road Map Initiative. In addition to biomarker discovery, the upgraded system will provide improved capabilities for characterizing multi-component protein complexes, discovering receptor-ligand pairs, elucidating regulatory proteins and signaling pathways, discovering DNA-transcription factor interactions, and performing peptide mapping for protein identification and characterization interactions. Detailed Summary of the Series4000 System and Photo.

Ciphergen Website/ProteinChip Series 4000 System

Protein Chip System with SELDI/MALDI interface to mass spectrometer 

In the near future, the ProteinChip interface will be installed on the Advanced Biosystems Q-Star Tandem Mass Spectrometer. This will provide the capability to conduct high performance protein identification, low molecular weight proteome phenotyping, and epitope mapping/protein interaction analysis. The interface affords superior mass accuracy thus differentiation between peptides, oligosaccharides, lipids, and EAM signals, while directly profiling for biomarkers in the low molecular weight proteome, can be accomplished.  Further, many peptides and small proteins can be directly identified, by performing ProteinChip ms/ms analysis. Elegant epitope mapping, receptor-ligand and other protein-protein interaction studies can also be performed when combined with ProteinChip Antibody Capture and pre-activated ProteinChip arrays.

Analytical and Preparative 2-D Gel Analysis

BioRad protean 2-D elecrophoresis sytem, FX Pro Plus Molecular Imager and PDQuest 2-D analysis software. Complex mixtures of cellular proteins or partially purified proteins will be resolved, imaged via radioisotopes, fluorescent dyes, tags or chemiluminescence and subsequently identified using protein SELDI-TOF chip technology, or LC/MS/MS.  

For fast 2-D gel analysis of a small amount of protein mixtures a 2-D system (Invitrogen) will be used.

Chromatographic Systems

HPLC and micro HPLC systems with detectors based on conductivity, UV-absorbance, light scattering, etc., using columns for size exclusion, hydroxylapatite, ion exchange (IE), reversed phase (RPC) affinity (AC) and   immunoaffinity (IAC) chromatography and an interface for LC/MS applications. The micro HPLC system will be hyphenated to MS/MS instrument and will be used for protein and peptide analyses and identification.

For very rapid IE-, RPC-, AC- and IA-chromatographic analyses, so-called CIM-disk and tube shaped monolithic columns will be used. Using this technology, analyses of even very complex protein mixtures can be performed in less than 5 minutes.

Peptide Synthesizer

Advanced ChemTech peptide synthesizer Model 496 MOS will be used for synthesis of peptides with up to 40-50 amino acids. After synthesis, the peptide with targeted sequence has purity between 80 and 95%. In a subsequent step, the peptide will be analyzed and purified using reversed-phase HPLC.   

Hybridoma Facility 

The hybridoma facility in the Division of Medical Oncology, in operation for 16 years, is part of COBRE CCRD.