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IO Informatics, Sage-N Integrate Proteomics Software for Microbial Studies, Biomarker Discovery

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By Uduak Grace Thomas

This article has been updated from a version posted March 6 to include comments from IO Informatics and Sage-N Research officials.

IO Informatics said this week that it will integrate its Sentient software suite with Sage-N Research's Sorcerer informatics appliance for proteomics analysis.

The combined product provides a semantics-based application that allows users to process mass spectrometry-based proteomics data for microbial research or biomarker discovery. The partners believe the system will eventually support automated screening for biological threats, and will also help researchers characterize the origin and type of disease.

Customers of the combined solution will receive both software tools linked via a set of application programming interfaces that are optimized to run on a Fujitsu server, Robert Stanley, president of IO Informatics, told BioInform.

The offering identifies microorganisms based on peptides present in biological samples and then semantically incorporates functional genomic and pathway information associated with each microorganism.

It also lets users cluster sequences into protein families, which can then be further enriched with annotations such as functional classification, related protein structures, and bacterial or virus-specific genes, as well as disease-related pathways.

The platform can be used to identify peptides from different microorganisms that have a common mechanism of action as well as to detect microbial pathogens before disease symptoms start to show, Ali Pervez, Sage-N Research's vice president of marketing, said in a statement.

'An Easy Decision'

This announcement marks IO Informatics' first partnership for the year and there are more to come, Robert Stanley, president of IO Informatics, told BioInform.

He said that this year the company of 10 intends to grow by forging additional partnerships with companies that have "complementary" capabilities.

"The culture and leadership at Sage-N is really impressive and a great fit with IO Informatics," he said. "They have done a fantastic job with the product they have and rather than spend five years developing what they have [ourselves] ... this is one of these cases where partnering to add value just makes perfect sense."

David Chang, Sage-N's CEO, told BioInform that the integration is in line with the trajectory of the proteomics research market.

"Over the last five years, proteomics research [has] grown in the sense that people don’t just do proteomics research, they do it in the context of pathogen detection or in the context of cancer research that ties into genomics or they do proteomics as part of a drug discovery platform that ties into metabolomics," he explained.

This means that customers now require tools that promote integration of data from multiple 'omics disciplines, he said.

It's no longer the case in cancer research, for example, that researchers perform proteomics experiments exclusively, he said. Currently, it's "one [leg] of a three-legged stool," which includes genomic analysis and imaging.

In this arrangement, Sage-N's Sorcerer system provides the tools to analyze peptides from microorganisms in LC-MSMS data, IO's Stanley explained. It also includes some intellectual property, which Sage-N licenses from the US Army, that identifies the source of these peptides by associating "a closeness of fit score" with each peptide detected in the data.

This score indicates the likelihood that a peptide in question comes from H1N1 or Escherichia coli, for example, he said.

This output is then transferred into IO's Sentient, where each peptide is enriched with data such as pathway information, associated diseases, and known treatments, Stanley said. This additional information makes it possible to "find biological activity that may be common to a family or a class of organisms, for example," he said.

Furthermore, combining peptide information with gene expression or metabolic signatures could be used to describe biomarker patterns that could serve as signatures for biological threats, he said.

He added that IO Informatics' Sentient product can be extended to include new data sources and link new applications into proteomics workflows as needed.

The companies have inked a joint venture agreement that allows either firm to sell both systems and the accompanying hardware as a single package so customers won't need to purchase separate licenses for the solution.

Stanley declined to provide details about pricing for the combined solution, although he did say that the licenses would cover both software and hardware.

This arrangement also puts IO Informatics ahead of competing firms like Cambridge Semantics, which offers some similar capabilities in terms of semantics but doesn't have the same breadth in terms of "text mining, statistics, proteomics analysis, genomics analysis, and database," Stanley said.

He added that a partnership strategy also lets IO focus on its forte: semantic integration of the data.

"We take the data directly into RDF and [then] we depend on our partners for all the rest," he said. "There are some competitors who try to do all of those things but you are not going to get the best solution with that route."

IO plans to announce a deal with a database vendor and statistical tool developer later this year, Stanley said. Additionally, the company has bagged some new pharmaceutical customers that it will also announce at a later date, he said.

For its part, Sage-N is working to develop a single platform solution that incorporates its existing software as well as third-party applications and will provide capabilities for "deep proteomics," Chiang told BioInform.

The final product, which will be released later this year, "links our traditional core competency in deep proteomics with other related things like statistical tools, visualization, microbial pathogen analysis, and [focuses] on deep data integration," he said.

The company may add to its headcount — which is currently about a dozen — at the end of the year, Chiang said.


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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