NEW YORK, Feb 14 – SciMagix, a Redwood Shores, Calif.-based bioinformatics company, unveiled its ProteinMine software for analyzing 2-d electrophoresis gels Wednesday.
The software is designed to search 2-d gels according to size, shape, location, and intensity of protein spots, in order to find combinations of protein patterns and protein expression patterns.
The software is designed to be used along with SciMagix' Scientific Image Management System, which stores, retrieves, and analyzes images.
“We created a product that does all sorts of visual searching of 2d gels,” said Suzanne Mattingly, marketing director for SciMagix. “Where other packages stop and we pick up is [the user] being able to click on any of the proteins in the gel and see whether any are upregulated or downregulated.”
This search is possible, said Mattingly, because each of the protein spots are quantitated, and the intensity, size and shape is registered when an image is entered into the database.
SciMagix developed Protein Mine in collaboration with Pfizer Global R&D, which now uses the software.
“Pfizer has been using the product in conjunction with the SIMS image data management system, and they are finding patterns that confer toxicity to certain compounds, said Mattingly. “They are able to search on patterns, and this saves virtually millions of dollars in not progressing compounds to the next step.”
Pfizer is also a customer of Compugen for its 2-D gel analysis software system, known as Z3. Z3 uses proprietary algorithms and color overlay technology to compare 2-D gel separations of proteins from normal and diseased tissues.
While having both the Z3 and the ProteinMine systems might seem redundant, Mattingly said the company is developing the SIMS system to be a meta-search platform, which can be used to search 2d gels across numerous systems.
“We want to come to the point where SIMS will be the base from which you can do searches of the gels,” she said.
The product will be available immediately, but SciMagix did not provide pricing information.