Services

The Proteomics Core will provide a comprehensive array of services pertaining to the design, performance and analysis of proteomic studies. The core not only offers the ability to implement and validate previously developed proteomic methods to profile proteins in biological fluids and tissues, to quantitate proteins, to idenity proteins and their posttranslational modifications, and to study protein-protein interactions, but also the capability to modify or develop entirely new assays when warranted. In addition, the core offers a full bioinformatics core for data management and analysis as well as new software development and the capability to perform a wide variety of genomic and high throughput assays. The core is already well equipped with a broad array of state-of-the- art analytical instrumentation for proteomic studies, which include an ABI 4700 MALDI-TOF/TOF mass spectrometer, a Ciphergen SELDI-TOF mass spectrometer, an Agilent 1100 Series LC/MSD mass spectrometer, a Beckman PF2D two-dimensional liquid chromatography system for protein fractionation, an Agilent 1100 Series Liquid chromatography system, a Beckman Biomek FX Robotic system, an Amerhsam Lucidea arrayer for protein and peptide microarrays, a Perkin Elmer ScanArray Express HT Laser Scanner, an Amersham ASP automatic hybridization station, anda Biomicrosystems Maui automatic hybridization station as well as state-of-the- art computational platforms including our own Macintosh X Serve Server that hosts our website (www.bidmcgenomics.org), all the databases and bioinformatics and statistical analysis tools. 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.

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.

• 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

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).
  

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

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.

• 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.

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