The Cancer Proteomics Core offers a comprehensive array of services pertaining to design, performance and analysis of proteomic and metabolomic studies with special emphasis on clinical samples and expertise in cancer biology and clinical cancer research. The core combines personalized project consultation and study design with comprehensive individualized bioinformatics support for data analysis and new software development.
Consultation is a major service of the facility. Initial consultation occurs at the project planning stage. Staff provides advice on study design, sample size, sample collection and handling and considers questions of clinical and biological relevance to cancer investigation. Close interactions continue throughout the project execution and analysis/interpretation phases. Consultation on all aspects of the project is particular critical for proteomics as workflows and sample processing for each project differ. To implement the optimal proteomics strategy it is crucial to understand the project and the anticipated results in detail. As a consequence, many hours of consultation are provided on project design, project adjustment based on results coming in and, most importantly, analyzing and performing systems biology on the data. The Facility Director or Co-Director participate in most consultations and are kept up-to-date on all ongoing projects by staff.
The core is well equipped with a broad array of state-of-the- art analytical instrumentation for proteomic studies, which include an AB/Sciex 4800 MALDI-TOF/TOF mass spectrometer, a Thermo LTQ Orbitrap XL-ETD mass spectrometer, an AB/Sciex 5500 QTRAP mass spectrometer, various HPLC and NanoLC systems, a Beckman Biomek FX Robotic system, a Perkin Elmer ScanArray Express HT Laser Scanner, as well as state-of-the- art computational platforms that host our website (www.bidmcgenomics.org), all the databases and bioinformatics and statistical analysis tools. The instrumentation is operated by the highly trained technical staff of the core laboratory. The Core has optimized all services and continues to improve on the established methods by carefully dissecting all parameters of each experimental process.
The Bioinformatics Core is the central portal of the Proteomics Core that provides DF/HCC investigators with access to phenotypically annotated proteomics and metabolomics 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 is 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.
Protein sample preparation and digestion
Protein and peptide profiling ofof bodily fluids and tissue or cell extracts
◦ Profiling by µLC/MS
Protein identification by µLC/MS/MS.
◦ coomassie& silver stained gel bands
Identification of protein and peptide post-translational modifications.
◦ phosphorylation sites
Protein-protein interaction (PPI) determination using antibody and tagged based IP-MS
Relative quantitation of proteins and peptides, including modified peptides, by µLC/MS/MS
◦ SILAC - stable isotope labeling of amino acids in cell culture which is a biosynthetic approach
New Services Offered
Quantitative proteomics: Relative and absolute protein quantitation applying isotopic, isobaric, and label-free methods such as iTRAQ, ICAT, SILAC, TMT, GIST, TIC ratio, and spectral counting.
Bioinformatics Analyses Offered