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Component: Bioinformatics

Component Bioinformatics focuses on data warehousing, implementation of data analysis and data mining tools, development of novel algorithms and databases in support of proteomic studies.

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Goals and Milestones

Highlights of activities for the current quarter

Methods and Results

Component Members

Goals and Milestones

The role of the Bioinformatics Component of the MCW NHLBI Proteomics Center is to manage the information flow from the project. To do this we will meet the following goals:

1. Produce and maintain the public and internal web sites for the MCW NHLBI Proteomics Center. A major function of the public web site (proteomics.mcw.edu) is to serve as the ‘public face’ of the MCW NHLBI Proteomics Center, providing overview and contact information for each of the other components of the MCW NHLBI Proteomics Center. Additionally, the public web site will provide access to data, protocols and bioinformatic tools developed by the project.
2. Produce and maintain a database of results from the proteomics and other experiments conducted as part of the project. Using a locally developed database schema based on the PEDRo standard, we have developed methods for capturing and storing the results of the wet lab experiments.
3. Integration of proteomics data with other databases. To aid in the interpretation of proteomic results, we will create connections into local rat databases such as the Rat Genome Database (link) and the MCW PhysGen (link) site in addition to external protein databases such as NCBI (link) and SwissProt (link). This will combine phenotype, genotype, expression data and proteomic data for a single model system. The extra information available via these resources will aid in the annotation and interpretation of proteins identified as being of interest via the MS/MS component.
4. Provide support for proteomics data analysis applications. We are installing the SEQUEST application for peptide identification on the MCW HPC cluster. We are also working with our BMS collaborators on facilitating post-peptide identification analysis of the results of MS based proteomics experiments.
   
5. Develop new methods and bioinformatic tools for the analysis of proteomic data. We are creating new algorithms and tools for the identification of peptides from MS data and the analysis of modified proteins. These tools will be made publicly available through this web site.
   

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