Institute of Cancer Research Uses Agilent Technologies’ HPLC/Chip MS System to Develop Protein Database

The Institute of Cancer Research (ICR) today announced the launch of the Center for Bioinformatic and Clinical Proteins (CBCP) Web site, which features a database containing information on 4,244 human proteins, including many related to cancer. The database, which was developed using Agilent Technologies’ (NYSE: A) HPLC-Chip/Mass Spectrometry (MS) system, will aid researchers in efforts to identify proteins and discover biomarkers associated with various types of cancer.

“This proteomics tool will help researchers investigate patterns of protein expression that are associated with cancer, and quickly trace characteristic changes in tissue back to the cell type from which they originated,” said Christopher Gerner, Ph.D., associate professor of Medical Biochemistry and principal investigator of the proteomics research team at the Institute of Cancer Research. “The database will help standardize proteomic analysis and facilitate greater understanding of the underlying pathophysiology of cancer.”

The proteins in the CBCP database, which are restricted to Swissprot entries to maximize reliability, currently focus on liver and colon cancers, melanoma and various forms of leukemia. Breast and lung cancer-related proteins will be added to the database in the near future. Researchers can use the database to test the suitability of particular proteins for use as biomarkers, evaluate the accessibility of proteins for identification by MS, and compare with their own proteomics data.

Researchers at ICR used various Agilent instruments and software to identify the proteins that comprise the database, including the 1100 Series LC system, XCT-Ultra ion trap MS with Chip-Cube-ESI and Spectrum Mill MS Proteomics Workbench software. In particular, the HPLC-Chip/MS was instrumental in building the database.

“The introduction of the HPLC-Chip/MS system tremendously improved our work,” said Gerner. “Through its higher separation performance, the system significantly increases peptide concentration during elution. It is also extremely robust and reliable; when monitored carefully, it successfully works 24 hours a day, seven days a week.”

Smaller than a credit card, the HPLC-Chip seamlessly integrates sample enrichment and separation capability of a nanoflow LC system with the intricate connections and spray tips used in electrospray mass spectrometry. The technology eliminates 50 percent of the fittings and connections typically required in an LC/MS system, dramatically reducing the possibility of leaks and dead volumes, significantly simplifying workflow, and increasing sensitivity and reliability during analysis.