Johns Hopkins University PROTEIN-DB2 Database System

Genomic data collection follows the workflow of amplification of DNA expression, amplified DNA extraction, high-throughput sequencing, and subsequent processing/analysis of the sequence data. DNA itself is a structurally stable molecule that can withstand cell lysis and remain relatively intact. Proteomic data collection, on the other hand, follows a more complex workflow, ranging from gel electrophoresis to mass spectrometry to liquid chromatography or a combination thereof. In addition, amplification of low-abundance proteins is much more difficult due to their level of expression and undesirable post-translational modifications that can occur outside the their normal environment. Therefore it is vital to keep track of all experimental conditions in proteomic data collection to ensure that the data collected truly represents the protein(s) of interest. While most laboratory information management systems (LIMS) do already handle the tracking of experimental conditions, they do not have the ability to store primary data and the subsequent analyses of that data. In addition, as proteomic data collection techniques become more refined and automated, the volume of data produced becomes much more diffcult to maintain control over. Description (Set) PROTEIN-DB2 is a relational database derived from the Protein Standards Initiative Object Model (PSI-OM). Within this database, users have the ability to store information related to a single experiment and compare data from multiple experiments, Information stored by the system includes primary n-dimensional gel image and mass spectrometry (MS) data on a fie server, along with commercial off-the-shelf analysis of the n-dimensional gel images, and MS in the database itself. In addition, the database has the capability of storing commercial off-the-shelf protein identification. The main goal of this database is to offer the user an environment suitable to extract knowledge about protein function and biological process mechanisms from a combination of data derived using many different techniques. Tools have been developed to extract data from third party software outputs (Nonlinear Dynamics, Progenesis Workstation, GE, Amersham, DeCyder, Shimadzu ect.) and transfer the information to the database. The system also contains several web-based interfaces for loading of the data to facilitate the end user, along with a web-based graphical query interface for gel spot information. The implementation of PROTEIN-DB2 leverages the programming language of Java 1.3+ for web forms, the graphical web interface, data parsing and loading. Proposed Use (Set) The design of the PROTEIN-DB2 database allows for the storage, visualization, and analysis of 2-D PAGE (poly-acrylamide gel electrophoresis, DIGE (difference gel electrophoresis) and MS (mass spectrometry) proteome data, as well as protein identification data produced from mass spec profiles by search engines such as Mascot. The tools and the database are scalable and meant to work on multiple operating systems

Inventor(s): Winslow, Raimond L

Type of Offer: Licensing



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