Thermo Develops Advanced Protein Identification and Quantitation Software

Thermo Electron Corporation, world leader in analytical instrumentation and software, has extended its protein identification and quantitation software package with the newly designed BioWorks™ 3.3.

Featuring unique PepQuan capabilities, BioWorks 3.3 enables automated quantitative analysis of iTRAQ™, SILAC™ and ICAT® labeled samples, as well as label-free quantitation techniques. A new probability-based scoring algorithm delivers increased confidence in protein identification. Additionally, a unified Search Results File (SRF) simplifies and accelerates the review and transfer of results by allowing all of the information to be stored in a single file. These powerful capabilities are detailed in a new brochure, which is available free of charge via http://www.accelacomm.com/jlp/tsp/35/10009993/.

With new pre-search and post-search filters, BioWorks 3.3 removes unwanted spectra from the search resulting in faster search times, allowing users to focus only on the proteins of interest. Reporting and documenting results is also improved with the new software package. Spectra and tables can be quickly and easily transferred to Microsoft® Office documents, while the new Protein Report feature enables printing of data directly from search results or the creation of PDF files.

BioWorks 3.3 features the SEQUEST® protein search algorithm, which automatically identifies proteins by comparing experimental tandem mass spectrometry (MS/MS) data with standard protein and DNA databases. It can analyze a single spectrum or an entire LC/MS/MS data set containing spectra from a mixture of proteins. The proprietary "cross-correlation" identification algorithm within SEQUEST extracts information and correctly identifies proteins even at low concentrations. Accurate mass capability is also incorporated in the new BioWorks 3.3 software package to enable SEQUEST searching on data acquired using Thermo's hybrid mass spectrometers.

The new software package can also process datasets acquired using vMALDI™ equipped LTQ XL™ systems Featuring enhanced SEQUEST Queue and Batch Search capabilities, users will also be able to launch searches on Mascot server from Bioworks 3.3 and compare SEQUEST and Mascot search results.

The new Bioworks 3.3 is the latest version of this software enabling protein identification and quantitation. Providing tools for automated analysis of iTRAQ labeled samples, as well as SILAC and metabolic labeling experiments, this software package offers increased confidence in protein identification.