Clinic Application of Proteomics Boston University Medical Campus Boston VA Research Institute 670 Albany St. Pathology 404 150 S. Huntington Ave. 1A Boston, MA 02118 Boston, MA 02130 jyang@bu.edu Jinghua.yang@va.gov Tel: (617) 414-7075 Tel: (857) 364-5611 Fax: (857)364-5627 Fax: (857)364-5627
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Our laboratory is pleased to provide facilities to investigators of Boston University Medical Campus and Boston VA Medical Center in clinic application of proteomics with expert, accurate, and collaborative interactions. Contracts and subcontracts from industries and other academic institutions are also welcomed. We provide our expertise with the following platforms:

1. Fluorescence-assistant Autoimmune Display (FaAD)

Application: Identification of autoimmune antigens from patients Description: Auto-immune diseases generate immune responses against patient’s own proteins. Tumors may also generate autoimmune responses. These immunogenic proteins are potential diagnostic and therapeutic targets. We will work with investigators to identify these antigens when the tissue biopsies and blood samples from the same patient are available. Briefly, the disease tissue will be resolved by two-dimensional gel and blotted onto membrane; the IgG from patients and healthy donors will be isolated and labeled with cy5 and cy3, respectively. Positive antigens will be differentially detected by 2D Western, visualized by Typhoon Imager and identified by mass spectrometry. The FaAD platform can be applied to:

- Tumors

- Autoimmune diseases

- Infectious diseases

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2. Differential Gel Electrophoresis (DiGE)

Application: Differential profiling of blood/tissue proteins from patients

DiGE Image

Description: Blood/tissue proteins from patients and healthy donors will be analyzed on the same 2D gel by labeling with different fluorescent dyes (Cy2, Cy3 and/or Cy5). Differentially expressed proteins will be quantitatively analyzed on the color-coded images using Typhoon Imager (GE Amersham). Interested spots will be identified with mass spectrometry (MALDI-TOF) following Trypsin digestion. We will work with you to identify blood/tissue markers using DIGE when blood/tissue biopsies are available from patients and matched donors.

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3. Fluorescence-assistant Multiple Dimensional HPLC (FaMD-HPLC)

Application: Differential profiling of blood/tissue proteins from patients

Description: FaMD HPLC is a new approach developed in our laboratory to differentially analyze whole protein samples from patients and healthy donors on multi-dimensional HPLC. In the similar way as DiGE, protein samples from patients and healthy donors will be labeled with Cy3 and Cy5, combined and analyzed on a 2-D Agilent HPLC equipped with two fluorescence detectors. With FaMD HPLC, we are able to fractionate whole blood/tissue proteins from patients and healthy donors in the same run, so that differentially expressed proteins can be quantitatively analyzed. The differentially expressed proteins will be in the liquid form and ready for mass spectrometry analysis.

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4. LS-MS/MS

Application: Protein Identification

Description: Our laboratory is equipped with 1) the Tempo™ nano LC followed with QSTAR Elite LC/MS/MS System (Q-TOF), and 2) Applied Biosystems VOYAGER-DE STR workstation (MALDI-TOF). These We do the following analysis:

- MALDI-TOF protein identification for samples isolated from 1-D or 2-D gels.

- Q-TOF protein identification for samples isolated from 1-D or 2-D gels.

- iTRAQ to identify differentially expressed proteins for less complicate samples.

- Date research and analysis.

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5. Luminex-based Multiplexed Marker Validation (LMMV)

Application: Validate a panel of markers in patient samples

Description: Luminex™ platform combines the efficiencies of multiplexing up to 100 different extracellular or intracellular markers for simultaneous analysis with similar reproducibility to ELISA methodology. The outcomes include the area under ROC for each marker and for a panel of markers.

We are currently planning to evaluate the specificity and sensitivity of a panel of colorectal cancer related blood markers.

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Our proteomics and mass spectrometry infrastructure and expertise are used in collaborations with colleagues at Boston University Medical Campus & Boston VA Medical Center and elsewhere.