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 information management and informatics platform. The company is now moving aggressively to get its system established in the marketplace and add to its capabilities.
Earlier this month, GenoLogics announced a partnership with Nonlinear Dynamics to integrate Nonlinear’s upcoming ProMST gel analysis platform into ProteusLIMS, which already supports Nonlinear’s Progenesis software. The company is also in talks with an undisclosed West Coast-based research institute about commercializing proteomics software developed there.
Academic proteomics facilities, in particular, may find ProteusLIMS appealing, both for its price and for its ability to interface with a broad range of mass specs and software packages.
“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 Biomolecular Resource Facility, who recently purchased ProteusLIMS. One of the selling points for him 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 about the system out. Contrary to traditional LIMS that have to be tailored to a user’s needs, ProteusLIMS already caters to proteomics workflows, he said, making it more suitable and less costly.
ProteusLIMS currently consists of three lab-management modules and three informatics modules. A base LIMS module, a workflow engine, and a web interface for interactions with customers and collaborators comprise the lab management part. On the data management 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 what to name files and where to place the data, for example. At present, the module integrates 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 also integrate the system with Thermo’s LTQ-FT. In addition, it is collaborating with other software groups to support open data formats such as the Institute for Systems Biology’s mzXML and the Protein Standard Initiative’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 GE Healthcare’s DeCyder.
Thirdly, the protein search management module allows researchers to integrate ProteusLIMS with protein database search engines, currently Mascot and Sequest. According to Bystrom, this module still requires users to upload search results manually, but the company plans to automate this part of the system.
GenoLogics is also working on additional modules, hoping to release ProteusLIMS 2.0 in mid-January. That version will include a new quantitation module that will likely offer the Xpress and ASAP Ratio software packages, 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 and pricing is planned for 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 anyway,” 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 ProteusLIMS 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 scheduled to be installed, at 11 sites, 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 adding to 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 with institutional investors from Canada and the US.
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 interface only with certain instruments.
Like many bioinformatics vendors, homegrown systems may be GenoLogics’ main competition, but not everybody is willing or able to do design their own proteomics LIMS — a fact that may work to the young company’s advantage. “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.
A version of this article originally appeared in BioInform’s sister publication ProteoMonitor.