A new PREMIER tool

PREMIER Biosoft acquires protein validation and quantification tool

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PALO ALTO, Calif.—Bioinformatics company PREMIER Biosoft hasbeefed up its mass spectrometry product portfolio with the acquisition ofProteoIQ, a comprehensive tool for comparative and quantitative proteomics,from NuSep, a firm in Australia.
NuSep is a 30-year-old, publicly listed life-science companythat sells products into the global bioseparations market. Its biologicalseparation techniques are based on its PrIME technology, which the companyclaims has produced a number of world firsts, including the world's first IVFsperm separation instrument. NuSep's research team has developed an extensiveportfolio of patented products. The company currently manufactures, distributesand sells 55 products to customers in the United States, Europe, Asia andAustralia.
In the somewhat opaque world of bioinformatics, PREMIER hassignificant credentials to boast of, according to company CEO Arun Apte, whonotes that the company now offers a broad spectrum of products for massspectrometry-based 'omics and imaging studies to the research community.
"We have been in the bioinformatics market for close to twodecades," Apte notes. "Our very first product, Primer Premier, was designed asa primer design tool for standard PCR. It was an instant success. Asinnovations happened, especially in the genomics area, we subsequentlydeveloped tools for cloning, qPCR and microarrays. Beacon Designer andAlleleID, our products for qPCR, have been installed in hundreds of labs aroundthe globe and are the only products on the market that support almost all thepopular qPCR chemistries. Array Designer is the only oligo design tool formicroarrays that supports gene expression to splice variant to tiling toresequencing arrays. We then forayed into mass spectrometry and authoredproducts for glycomics and lipidomics, the new 'omics on the market. We builtpartnerships with large mass spec companies to place our products in the handsof the users. Last year, we released MALDIVision, an MS imaging solution, aswell. It is the only tool on the market to support 10GB MALDI imaging data."
Now, with the NuSep acquisition, PREMIER has entered theattractive proteomics market.
"For the rapidly growing proteomics market, ProteoIQ is astrategic fit to PREMIER Biosoft's existing mass spec product offering, andhelps consolidate our position as a leader for providing informatics tools formass spectrometry," says Apte. "Before the NuSep acquisition, a major productthat was missing from our mass spec portfolio was a proteomics tool. We zeroedin on ProteoIQ by looking at the comprehensive functionality it offered. The toolis capable of analyzing hundreds of LC-MS and LC-MS/MS runs that containthousands of MS/MS spectra to validate, quantitate, annotate and comparepeptides and proteins across samples."
ProteoIQ is a software tool for proteomic data analysis thatstreamlines the process of statistical validation, protein quantification andcomparative proteomics on one platform. It supports validation of the proteinsidentified by other database search tools such as Mascot, SEQUEST or X!Tandem.ProteoIQ incorporates the False Discovery Rate and Protein Probabilityapproaches for statistical validation of identified proteins. It performsquantitative analysis via spectral counting, precursor intensity, iTRACQ, TMT,SILAC and iCAT workflows. Users can quickly perform differential analysis ofresults across biological samples thereby facilitating identification ofputative biomarkers. ProteoIQ calculates global False Discovery Rate tocalculate an error rate for peptide identifications by searching Peptide MS/MSspectra against a decoy database and comparing the results with the normaldatabase search results. FDR defines an error rate for all results even thoughit does not pinpoint the identifications that are false. FDR is the most robustapproach for small data sets, Apte claims.

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