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Submitted on January 1, 2005
Revised on May 31, 2005
Accepted on June 3, 2005

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a QqTOF mass spectrometer: 2. New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets

Robert J. Chalkley, Peter R. Baker, Lan Huang, Kirk C. Hansen, Nadia P. Allen, Michael Rexach, and A L. Burlingame

Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143-0446

Corresponding Author: chalkley{at}cgl.ucsf.edu

A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was carried out by a multidimensional chromatography strategy of strong cation exchange fractionation of peptides followed by reverse phase LC-ESI-MSMS using a QSTAR. This dataset was then analyzed using the latest developmental version of Protein Prospector. The Prospector search results were also compared with results from the search engine ‘Mascot’ using a new results comparison program within Prospector named ‘SearchCompare’. The results from this study demonstrate that the high quality data produced on a QqTOF geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines.


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