The Cancer Proteomics Core provides high-sensitivity, resolution, and throughput proteomics
methods. The Core focuses on proteomic approaches to translational research based on analysis
of patient materials such as blood, urine, and tumor tissue extracts.

Director: Towia Libermann, Ph.D.
Phone: (617) 667-3393
Email: tliberma@bidmc.harvard.edu

Other Staff:

Mass Spectrometry Proteomics: John Asara, Ph.D.
Phone: (617) 667-6182
Email: jasara@bidmc.harvard.edu

Clinical Proteomics: Dimitrios Spentzos, M.D.
Phone: (617) 667-0760
Email: dspentzo@bidmc.harvard.edu

Research Proteomics: Luiz Zerbini, Ph.D.
Phone: (617) 667-0760
Email: lzerbini@bidmc.harvard.edu

Bioinformatics: Hasan Otu, Ph.D.
Phone: (617) 667-0808
Email: hotu@bidmc.harvard.edu

Location of Core:

The facility is located at 4 Blackfan Circle, HIM 208, Boston.

Major Equipment:

Technologies deal for high-throughput screening of clinical samples.

• High-performance ABI 4700 MALDI-TOF/TOF mass spectrometer. Protein
  identification by extremely fast, automated MALDI-TOF peptide mass fingerprinting.
• Protein profiling and identification by SELDI (Surface-Enhanced Laser Desorption/
  Ionization) Time-Of-Flight mass spectrometer by Ciphergen. The Ciphergen Protein
  Chips® technology uses different chromatographic surfaces for separation, detection
  and analysis of complex mixtures of proteins at femtomole levels).

• 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.

High performance protein factionation by Beckman PF2D LC Fractionation System.

High resolution LC by Dionex Nano LC Dual Gradient Capillary Separation System. The
system will significantly increase the number of proteins that can be identified in clinical
samples such as serum or tissue extracts and will be essential for identifying peptides with
post-translational modifications and for separating isotope labeled proteins for protein
quantitation.

Automated liquid handling by Beckman Biomek FX Robotic system.

Microarray Facility for protein and peptide microarrays utilizing an Amersham Lucidea
arrayer. Hybridization stations by Amersham ASP automatic hybridization station, and a
Biomicrosystems Maui automatic hybridization station. Arrays scanned by Perkin Elmer
ScanArray Express HT Laser Scanner.

Proteomics Services:

• Protein profiling of complex biological samples, eg. serum, urine, tissue, cell extracts.
  • Profiling by µLC/MS.
  • Multidimensional protein fractionation by µLC.
• Protein identification by µLC/MS/MS.
  • coomassie & silver stained gel bands.
• Identification of protein and peptide modifications.
  • phosphorylation sites.
  • protein modifications such as acetylation, methylation, and ubiqitination.
  • By µLC/MS/MS.
  • coomassie stain only, purified proteins.
• Relative quantitation by µLC/MS/MS
  • SILAC - stable isotope labeling of amino acids in cell culture which is a biosynthetic approach.
  • GIST - global internal standard technology, a post digestion peptide level labeling
    technique.
  • ICAT - isotope coded affinity tag -based protein profiling.
  • ITRAQ - isobaric peptide tagging system that enables you to label all primary
    amines, regardless of peptide class.

Bioinformatics Analyses Offered:

• Personalized consulting
• Customized data analysis and interpretation
• Web-based bioinformatics tools
• Comprehensive and innovative Bioinformatics and visualization tools
• Comprehensive annotation tools
• Identification of Global Relationships
• Incorporation of Biological Knowledge
• Pathway Analysis
• Publication ready figures
• The Bioinformatics Core is also responsible for software support and development.

To access the core, please contact Towia Libermann at (617) 667-3393 or by email at
tliberma@bidmc.harvard.edu.

http://www.dfhcc.harvard.edu/core-facilities/cancer-proteomics/