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A more recent version of this article appeared on August 1, 2005. Originally published In Press as doi:10.1074/mcp.D500001-MCP200 on May 27, 2005.
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Submitted on January 1, 2005
Revised on April 27, 2005
Accepted on May 27, 2005

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a QqTOF mass spectrometer: 1. How much of the data is theoretically interpretable by search engines?

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

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

Corresponding Author: robertc{at}itsa.ucsf.edu

An in-depth analysis of a multidimensional chromatography – mass spectrometry dataset acquired on a QqTOF geometry instrument has been carried out. A total of 3269 CID spectra were acquired. Through manual verification of database search results and de novo interpretation of spectra 2368 spectra could be confidently determined as predicted tryptic peptides. A detailed analysis of the non-matching spectra was also carried out, highlighting what the non-matching spectra in a database search typically are composed of. The results of this comprehensive dataset study demonstrate that QqTOF instruments produce information-rich data, of which a high percentage of the data is readily interpretable.


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