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A new PREMIER tool
April 2013
by Lloyd Dunlap  |  Email the author


PALO ALTO, Calif.—Bioinformatics company PREMIER Biosoft has beefed up its mass spectrometry product portfolio with the acquisition of ProteoIQ, a comprehensive tool for comparative and quantitative proteomics, from NuSep, a firm in Australia.
NuSep is a 30-year-old, publicly listed life-science company that sells products into the global bioseparations market. Its biological separation techniques are based on its PrIME technology, which the company claims has produced a number of world firsts, including the world's first IVF sperm separation instrument. NuSep's research team has developed an extensive portfolio of patented products. The company currently manufactures, distributes and sells 55 products to customers in the United States, Europe, Asia and Australia.
In the somewhat opaque world of bioinformatics, PREMIER has significant credentials to boast of, according to company CEO Arun Apte, who notes that the company now offers a broad spectrum of products for mass spectrometry-based 'omics and imaging studies to the research community.  
"We have been in the bioinformatics market for close to two decades," Apte notes. "Our very first product, Primer Premier, was designed as a primer design tool for standard PCR. It was an instant success. As innovations happened, especially in the genomics area, we subsequently developed tools for cloning, qPCR and microarrays. Beacon Designer and AlleleID, our products for qPCR, have been installed in hundreds of labs around the globe and are the only products on the market that support almost all the popular qPCR chemistries. Array Designer is the only oligo design tool for microarrays that supports gene expression to splice variant to tiling to resequencing arrays. We then forayed into mass spectrometry and authored products for glycomics and lipidomics, the new 'omics on the market. We built partnerships with large mass spec companies to place our products in the hands of the users. Last year, we released MALDIVision, an MS imaging solution, as well. It is the only tool on the market to support 10GB MALDI imaging data."  
Now, with the NuSep acquisition, PREMIER has entered the attractive proteomics market.
"For the rapidly growing proteomics market, ProteoIQ is a strategic fit to PREMIER Biosoft's existing mass spec product offering, and helps consolidate our position as a leader for providing informatics tools for mass spectrometry," says Apte. "Before the NuSep acquisition, a major product that was missing from our mass spec portfolio was a proteomics tool. We zeroed in on ProteoIQ by looking at the comprehensive functionality it offered. The tool is capable of analyzing hundreds of LC-MS and LC-MS/MS runs that contain thousands of MS/MS spectra to validate, quantitate, annotate and compare peptides and proteins across samples."  
ProteoIQ is a software tool for proteomic data analysis that streamlines the process of statistical validation, protein quantification and comparative proteomics on one platform. It supports validation of the proteins identified by other database search tools such as Mascot, SEQUEST or X!Tandem. ProteoIQ incorporates the False Discovery Rate and Protein Probability approaches for statistical validation of identified proteins. It performs quantitative analysis via spectral counting, precursor intensity, iTRACQ, TMT, SILAC and iCAT workflows. Users can quickly perform differential analysis of results across biological samples thereby facilitating identification of putative biomarkers. ProteoIQ calculates global False Discovery Rate to calculate an error rate for peptide identifications by searching Peptide MS/MS spectra against a decoy database and comparing the results with the normal database search results. FDR defines an error rate for all results even though it does not pinpoint the identifications that are false. FDR is the most robust approach for small data sets, Apte claims.
Code: E041313



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