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Mol Cell Proteomics. 2005 Aug;4(8):1189-93. Epub 2005 May 27.

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?

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1
Mass Spectrometry Facility, University of California San Francisco, San Francisco, California 94143-0446, USA. robertc@itsa.ucsf.edu

Abstract

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.

PMID:
15923566
DOI:
10.1074/mcp.D500001-MCP200
[Indexed for MEDLINE]
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