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Originally published In Press as doi:10.1074/mcp.D500002-MCP200 on June 3, 2005.
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Molecular & Cellular Proteomics 4:1194-1204, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Dataset

Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting, Quadrupole Collision Cell, Time-of-flight Mass Spectrometer

II. New Developments in Protein Prospector Allow for Reliable and Comprehensive Automatic Analysis of Large Datasets*,S

Robert J. Chalkley{ddagger},§, Peter R. Baker{ddagger}, Lan Huang{ddagger},¶, Kirk C. Hansen{ddagger}, Nadia P. Allen||, Michael Rexach|| and Alma L. Burlingame{ddagger}

From the {ddagger} Mass Spectrometry Facility, University of California, San Francisco, California 94143-0446 and the || Department of Biological Sciences, Stanford University, Stanford, California 94305-0155

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 instrument. 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 quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines.

§ To whom correspondence should be addressed: University of California, 521 Parnassus Ave., Rm. C-18, San Francisco, CA 94143-0446. Tel.: 415-476-5189; Fax: 415-502-1655; E-mail: robertc{at}itsa.ucsf.edu


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