As proteomics facilities are churning out growing piles of mass spectra, gel images, and hit lists, GenoLogics is aiming to jump into the niche of proteomics data management.
Earlier this year, the Canadian bioinformatics firm, a spin-out of the University of Victoria, launched the first version of ProteusLIMS, its proteomics lab information management and informatics platform. The company is now moving aggressively to get its system established and add to its capabilities.
Last week, GenoLogics announced a partnership with Nonlinear Dynamics to integrate Nonlinear’s upcoming ProMST gel analysis software into ProteusLIMS, which already supports Nonlinear's Progenesis software. The company is also in talks with an undisclosed West Coast-based research institute about supporting and integrating proteomics software developed there.
Academic proteomics facilities may find ProteusLIMS especially appealing, both for its price and for its ability to interface with many other companies' products, like mass specs or software.
“There are a lot of LIMS companies out there, but they are mostly targeted to big pharma,” said Alexander Kurosky, director of the University of Texas Medical Branch NHLBI Proteomics Center, who recently purchased a ProteusLIMS platform.
One of the selling points for Kurosky was that ProteusLIMS supports software that he has already been using, including gel analysis tools from Nonlinear, and mass spec software from Genomic Solutions.
“We certainly knew that we could not afford any of the commercially available LIMS systems, which are generally well in excess of $100,000,” said Cory Bystrom, director of the Oregon Health Sciences University Proteomics Core Lab who recently decided to buy the system after beta-testing it for one year.
The list price for ProteusLIMS typically ranges from $120,000 to $500,000, depending on the configuration, support, and licenses. “It's more than just a LIMS system, it also integrates proteomics scientific data,” said James DeGreef, GenoLogics' product manager, who just returned from a two-week East Coast trip to get the word out about the system. ProteusLIMS caters to proteomics workflows, he said, making it more suitable and less costly than traditional LIMS, which have to be tailored to a user's needs.
ProteusLIMS currently consists of three lab management modules and three informatics modules. The lab management component comprises a base LIMS module, a workflow engine, and a web interface for interactions with customers and collaborators. On the data-management and informatics side, there is a mass spec module, a gel module, and a protein search-management module.
The mass spec module interacts with mass spectrometers, telling the instruments, for example, what to name files and where to place the data. At present, the module is compatible with “pretty much all” of Applied Biosystems' mass specs, DeGreef said, as well as some instruments from Waters and Thermo. The company is currently working to integrate with Thermo's LTQ-FT. In addition, it is collaborating with other software groups to support open-source standards such as ISB's mzXML and PSI's mzData.
The gel module deals with all aspects of 1D and 2D gel analysis. It currently only interfaces with Nonlinear's Progenesis software, but the company is working on also supporting Bio-Rad's PDQuest and Amersham's DeCyder.
Thirdly, the protein search-management module allows researchers to integrate protein database search engines, currently Mascot and Sequest. According to Bystrom, GenoLogics is still working on making the protein search manager a more automated part of the system, which currently requires him to upload search results.
But GenoLogics is also working on additional modules, hoping to release ProteusLIMS version 2.0 in mid-January. That version will have a quantitation module added that will likely offer Xpress and ASAP Ratio, both from ISB. Later, it might also include MSQuant from Matthias Mann's lab and ProICAT/ProQuant from ABI. An account management module that will deal with scheduling, pricing and billing is planned for mid-March.
The company is also working on a separate proteomics analytics platform, to be called ProteoMiner, an add-on to ProteusLIMS. This product, which will address, for example, complex searches, multi-dimensional data mining, and visualization of large data sets, is set to be released by the middle of next year.
“They are a bit of a work-in-progress-company, as almost all the software is in proteomics anyways,” said Kurosky. “It's not a finished, turn-key product, and I think it will take time, but we would like to work with them.”
The product has already changed considerably: “It's developed dramatically over the last year, and it's a very nice piece of software now,” said Bystrom.
At present, ProteusLIMS is installed, or will be installed, at 11 sites in total, most of them academic institutions. But GenoLogics is also in discussion with several pharmaceutical companies, according to DeGreef.
To handle the development and marketing, the 14-employee company is currently ramping up its staff, filling at least six new positions.
GenoLogics was founded three years ago with backing from angel investors, Genome British Columbia and Genome Canada. It has since raised an undisclosed amount of venture capital from BC Advanced Systems Institute and the Canadian National Research Council and is currently finalizing a “quite substantial” Series A round of venture-capital financing with institutional investors from Canada and the US.
Systems built in-house may be GenoLogics' main competitors. However, not everybody is willing or able to design their own LIMS. “Developing your own software, if you can do it, that's great … but it takes a lot of time and a lot of effort and personnel,” said Kurosky.
Other competitors include LabVantage, which has a partnership with Matrix Science and offers a LIMS called Sapphire Proteomics Industry Solution Accelerator, and freely available systems, such as the National Cancer Institute's caLIMS, along with proprietary LIMS systems that only interface with certain instruments and generic LIMS systems.
— JK