Proteomics

Proteomics, the analysis of proteins in samples of bodily fluid or tissue, is fundamental to BG Medicine’s biomarker discovery capability. Protein mass spectrometry forms the core of our proteomics measurement platform. This proteomics workflow is based on multi-dimensional liquid chromatography (LC), chemical isotopic peptide labeling, and matrix-assisted laser desorption ionization (MALDI) mass spectrometry analysis of peptides generated from extremely small starting volumes of biological sample. We have refined the workflow to achieve coefficients of variation consistently less than 15% for proteins identified in human and animal studies. Sophisticated proprietary informatics tools developed at BG Medicine are able to identify specific protein variants and generate detailed protein sequence information which may be associated with disease or drug response. In addition to mass spectrometry-based proteomics, BG Medicine conducts proteomic analyses using microformat, multiplexed immunoassay technologies which allow for the targeted measurement of proteins present at extremely low concentrations.

In performing proteomic measurements over many years, BG Medicine has established extensive proprietary databases of identified and characterized proteins found in bodily fluids and tissues, across many diseases and treatments. This catalogue reduces the time required for full protein identification and characterization and continues to grow with every project.

Strategy

• Maximize the number of reproducibly quantified and identified components
• Peptide-based proteomics strategy
• Protein identification by multi-dimensional LC-MS/MS (primarily MALDI ionization-based)
• Peptide/protein quantification by 4-plex iTRAQ™ stable isotope labeling
• Sample requirements: 25-50 μl plasma per sample, 20 mg tissue per sample
• Proprietary data processing pipeline for: 
• peptide-protein assignment
• protein quantification
• data normalization
• protein polymorphism characterization