A RESOURCE FOR CONSTRUCTION OF 2D GEL PROTEIN DATABASES

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The long-term objective of the QUEST resource facility at the Cold Spring Harbor Laboratory is to develop 2D gel protein databases as powerful tools for biological research. Specifically, this facility seeks 1) to further develop the computer technology for analysis of two-dimensional protein gels, 2) to build model protein databases in three important research areas, and 3) to disseminate these databases in a form that other researchers can use on personal computers. The QUEST resource is really two resources in one. On the computer side, the software developers will seek to make 2D gel image analysis almost totally automatic, and they will seek to improve the productivity of the scientists who build protein databases by improving the user interface and the database management tools. On the laboratory side, the members of the QUEST facility will perform core and collaborative experiments to build protein databases and to identify large numbers of the proteins detected on two dimensional gels. Databases will be developed for the following research areas: 1) cell- proliferation in mammalian cells, 2) nuclear gene-regulatory proteins, and 3) yeast cell and molecular biology. Each protein database builds on previous experience at the QUEST facility and on the scientific research of core and collaborative workers. The QUEST laboratory will include a protein chemistry facility for protein identifications. Microsequencing will be used routinely to identify proteins from two-dimensional gels. Antibodies will be collected and used to identify proteins of current interest. Peptide profiles and amino acid compositions will provide additional information to relate the protein maps from different species and from different laboratories. The QUEST protein databases will be disseminated to other researchers on CD-ROM disks for use on Macintosh computers. Gel images, quantitative data, annotations, and laboratory records will be provided for each experiment. The data will be compatible with Hypercard and numerous software packages for statistical analysis and data presentation that are now available on the Macintosh. As a technology to study the normal and disease-related protein profiles of cells and body fluids, 2D gel protein databases will have both immediate and long-term impact on health problems. Already marker proteins for diseases such as leukemias have been found. In the long term, automated 2D gel analysis, coupled with extensive protein databases, should give diagnoses based not just on marker proteins but on the entire protein profile including genetic polymorphisms, altered regulatory proteins (oncogene products), and responses to external agents (viruses, stress, drugs).