If scientists thought genomics created a data bottleneck, what about proteomics?
Researchers trying to make sense of proteins often run thousands of gel samples per experiment. Each gel may have up to 800 spots worthy of further investigation, creating as many as 800,000 data points for a single experiment. If one of these spots proves to be novel and is a target for a drug, the ability to go back through each step in the drug discovery process is essential.
Then the difficulties really begin: What was the original starting material? How was it prepared? How can I prove I actually found something novel? Scientists need to be able to answer these questions and back their answers up with documented research.
In an effort to make this easier, Genomic Solutions of Ann Arbor, Mich., has developed Protein Warehouse, software that integrates all the pertinent information for tracking a protein through the drug discovery process. The program enables scientists to perform automated database searches of all data generated along the proteomic pathway, enhancing their understanding of protein behavior.
“The day to day running of a lab with a high throughput gives you insight into what you have to do in order to capture all the data you need,” said Jon Klein, director of the proteomics laboratory at the University of Louisville School of Medicine, one of the core proteomics labs Genomic Solutions has been working with as it develops the product.
“The whole process of running 400 or 500 gels in short order gives you a new perspective into what software tools you need to do good sample tracking and make data usable,” Klein said.
Protein Warehouse will be released as a beta product in December to six new customers. The University of Louisville will be among the first to beta test the software.
Although there are other LIMS systems available on the market today, few were designed specifically for the proteomics process, according to Christine Ethier, vice president of the company’s proteomic business unit.
The Protein Warehouse application, which uses an SQL engine as its core database, integrates data collection, central storage, querying, and reporting into one environment. Its multi-user, multi-protect environment is intended to speed data entry and ensure data integrity.
Protein Warehouse tracks data from all experimental protocols down to the protein feature level. Two-dimensional gel image and corresponding protein feature data are imported simultaneously. Sample entry data enables the user to track the samples and corresponding users, gels, instrumentation, and data.
Built for data mining purposes, the software is designed to help expedite analysis, reporting, and troubleshooting. Protein Warehouse was developed to help a researcher get various projects to “talk” to each other. And the software can capture all aspects of proteomics data, such as gel image and amino acid sequences.
Genomic Solutions hopes to integrate genomic and proteomic tools, such as Protein Warehouse, with its equivalent genomic tool, GeneTAC Integrator. Initially, the company will have all its products feeding information into the database.
In the next phase, it hopes to work with mass spec companies to incorporate its data into Protein Warehouse. In the long term, it anticipates seeing bi-directional communication between its instruments and major mass spec instruments.
Genomic Solutions, which recently divested itself of its mass spectrometer business, has decided to concentrate on developing software and other proteomics and genomics instruments that can be used in conjunction with any mass spec machine on the market.
The company also offers contract services for proteomic and genomic research. These non-royalty-based services don’t charge royalty fees for drugs developed from the targets that are found.