Identifying Post-Translationally Modified Proteins Has Never Been Easier

BIOINQUIRE, LLC today announced the release of ProteoIQ, version 1.2, an innovative and time-saving bioinformatics tool for the analysis of proteomic data. The newest version of ProteoIQ provides researchers with automated methodology for identifying proteins that possess post-translational modifications in a manner that was not previously possible.

New functionality included in ProteoIQ v. 1.2 is specifically designed for researchers using proteomic strategies that involve separations at the protein level followed by digestion and separation at the peptide level, such as Gel-C-MS/MS. “Current proteomic software was designed for analyzing 2D-gel or MudPIT data, and is not optimal for Gel-C proteomic workflows,” said James Atwood III, Chief Operating Officer and co-founder of BIOINQUIRE.

“Comparing the experimental and theoretical molecular weights for the intact proteins identified in a Gel-C experiment enables my lab to quickly identify glycosylated proteins, as these appear at a higher molecular weight than the one calculated solely from the protein’s amino acid sequence,” said Ron Orlando, University of Georgia biochemist , who uses mass spectrometry for the analysis and characterization of proteins and glycoproteins. “ProteoIQ v. 1.2 quickly identifies truncated and degraded proteins as their experimental masses are below the calculated values. To the best of my knowledge, the information gained by the protein separation is lost in other commercial software packages.”

“Our aim with ProteoIQ was to provide a bioinformatics tool that enables researchers to quickly identify meaningful results from mounds of proteomic data. ProteoIQ v. 1.2 is an extension of this philosophy and brings a new dimension to proteomic data analysis,” said D. Brent Weatherly, Chief Executive Officer and co-founder of BIOINQUIRE.

ProteoIQ v. 1.2, is particularly well-suited for comparative proteomic analyses, where spectral counting-based quantification is combined with data mining functions to enable researchers to find differences between multiple proteomic data sets. The software generates statistically validated protein sets, which can then be compared. For example, proteins that are different across multiple samples can be easily identified using the difference function. Taking the intersection of two proteomes allows the researcher to obtain expression levels of those proteins in common.

ProteoIQ v.1.2 will be unveiled at the 2009 International Symposium by the Association of Biomolecular Resource Facilities (ABRF), February 7 - 10, 2009 in Memphis, TN, and is available on the company website for scientists not attending this conference. Current ProteoIQ users can upgrade their current software to v1.2, free of charge, at the same website.