DF/HCC Cancer Proteomics Core

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Dana Farber/Harvard Cancer Center

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Proteomic Technologies

The core is already well equipped with a broad array of state-of-the-art analytical instrumentation for proteomic studies, which include

  • ABI 4700 MALDI-TOF/TOF mass spectrometer
  • Ciphergen SELDI-TOF mass spectrometer
  • Agilent 1100 Series LC/MSD mass spectrometer
  • Detailed protein structural characterization using tandem mass spectrometry in microcapillary LC/MS/MS mode to fully characterize potential target proteins for sequence and post-translational modifications with lower throughput
    • ABI QSTAR Pulsar Hybrid mass spectrometer for LC/MS/MS
    • Electro spray MS by Thermo Finnigan LCQ Deca Ion Trap Mass Spectrometer for LC/MS/MS

  • Beckman PF2D two-dimensional liquid chromatography system for protein fractionation
  • Agilent 1100 Series Liquid chromatography system
  • High resolution LC by Dionex Nano LC Dual Gradient Capillary Separation System
  • Beckman Biomek FX Robotic system
  • Amerhsam Lucidea arrayer for protein and peptide microarrays
  • Amersham ASP automatic hybridization station
  • Biomicrosystems Maui automatic hybridization station
  • Perkin Elmer ScanArray Express HT Laser Scanner

The instrumentation will be operated by the highly trained technical staff of the core laboratory. The core has also developed standard procedures for quality control to assure the timely delivery of accurate and high quality data. The core will implement procedures for the proper handling, processing and storage of proteomic samples.

Bioinformatics Core

The Bioinformatics Core will be the central portal of the Proteomics Core that will provide DF/HCC investigators with access to phenotypically annotated proteomics data as well as a large set of analytic procedures (i.e. unsupervised and supervised learning techniques, statistical analysis tools, automated clustering and classification procedures, pathway analysis and generation tools, protein identification database tools, data-visualization tools, annotation tools) with which to explore the data sets for further hypothesis generation.

Finally, a consultative service provided by key members of the core will be available at all times for DF/HCC investigators to assess the rationale and feasibility for undertaking specific projects, designing proteomic studies, process and protocol development, proteomic data analysis, and the interpretation of results.



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