BioWorks 3.3.1

• ETD Preprocessing for quick and easy searching of ETD data
• Import of Mascot data and comparison of SEQUEST and Mascot results
• PepQuan for quantitative analysis
• Probability-based scoring algorithm for SEQUEST
• More pre-search and post-search filters
• Enhanced reporting functionality

SEQUEST is one of the most sensitive searching algorithms available, ensuring that no important protein is missed in searches.  SEQUEST automatically identifies proteins by comparing experimental tandem mass spectrometry (MS/MS) data with standard protein and DNA databases. SEQUEST determines the amino acid sequence and thus the proteins that correspond to the mass spectrum of the peptide being analyzed. SEQUEST can analyze a single spectrum or an entire LC/MS/MS peptide map containing a mixture of proteins automatically.  The proprietary "cross-correlation" identification algorithm within SEQUEST can extract information and correctly identify proteins even from low concentrations that generate a weak signal.  This is especially useful when protein samples sizes are limited and the signal-to-noise ratio is low.  SEQUEST is designed for accurate mass analysis of peptides and proteins on the LTQ Orbitrap and LTQ FT hybrid systems.  BioWorks 3.3.1 has accurate precursor and fragment mass tolerances for SEQUEST that allow for more accurate determination of peptides with increased speed and confidence.

Our probability-based scoring algorithm allows all of the traditional SEQUEST sensitivity complemented by the stringency of our new probability-based algorithm.  The probability scoring allows BioWorks to prioritize and rank the SEQUEST hits and give users the flexibility to get ALL of their results while knowing that false positives are not a concern.

BioWorks 3.3.1 is specifically designed to work with the Thermo Scientific LTQ XL with ETD.  Thanks to the ETD preprocessing employed by BioWorks, customers can process peptides created with different proteases and be assured that SEQUEST is able to quickly, easily and confidently process the data.

BioWorks 3.3.1 also allows users to import Mascot results to the BioWorks grid after a SEQUEST search has been run.  This allows users to easily compare the results of these two search algorithms and to export the results.

PepQuan is the quantitation feature of BioWorks, providing functionality for iTRAQ analysis using either PQD or HCD, SILAC analysis, ICAT analysis or the Area/Height Calculation for a quick semi-quantitative assessment of the abundances of individual proteins and peptides.  The MS-based algorithms have been integrated with the ICIS peak detection algorithm from Xcalibur.  BioWorks 3.3.1 also has a Quan View for better viewing and export of quantitative results.

BioWorks 3.3.1 allows users to employ a new unified search results file (.SRF) or to choose the traditional SEQUEST DTA and OUT file format.  The new SRF file is a single binary file that allows all of the information to be stored in a single file, thus simplifying and accelerating data access.  This file format, in addition to other changes in the software, makes SEQUEST significantly faster than before.

BioWorks 3.3.1’s results layout allows the user to interrogate protein and peptide results more interactively than before, with the ability to filter, sort, merge and remove proteins from the list.  Filtering options include both pre-search filters and post-search filters. The pre-search filters remove unwanted spectra from the search, thereby reducing the search time, while the multitude of protein and peptide post-search filters now available will allow the user to focus only on the proteins of interest. Display Ions has been improved for better resolution and zooming.  BioWorks not only has SEQUEST Summary for single SEQUEST searches, but also MultiConsensus Report for looking at multiple SEQUEST searches or LC runs and Protein Comparison View for looking at differences between two different searches.

BioWorks 3.3.1 has been designed for easier exporting and reporting of data.  The spectra and tables in BioWorks are quickly and easily transferred to Microsoft Office documents making it easy for users to submit a publication, grant application or other communication.  BioWorks 3.3.1 has a Protein Report feature to easily print data from search results or to create a PDF file with the appropriate information.  It has never been easier to get results from the screen and into a document!

BioWorks 3.3.1 also includes the following additional software features:

• Compatibility with HUPO mzData format
• New features for accurate mass SEQUEST searching
• Reverse Database Searching
• Protein and Peptide Comparison functions   
• Enhanced SEQUEST Batch Search         
• And much more...