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Originally published In Press as doi:10.1074/mcp.D500001-MCP200 on May 27, 2005.
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Molecular & Cellular Proteomics 4:1189-1193, 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

I. How Much of the Data is Theoretically Interpretable by Search Engines?*,S

Robert J. Chalkley{ddagger},§, Peter R. Baker{ddagger}, Kirk C. Hansen{ddagger}, Katalin F. Medzihradszky{ddagger}, Nadia P. Allen, Michael Rexach and Alma L. Burlingame{ddagger}

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

An in-depth analysis of a multidimensional chromatography-mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument was 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.

§ To whom correspondence should be addressed: University of California San Francisco, 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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