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?

Mol Cell Proteomics. 2005 Aug;4(8):1189-93. doi: 10.1074/mcp.D500001-MCP200. Epub 2005 May 27.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Chromatography, Liquid*
  • GTP-Binding Proteins / chemistry*
  • GTP-Binding Proteins / metabolism
  • Humans
  • Peptide Fragments / analysis*
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization*

Substances

  • Peptide Fragments
  • GTP-Binding Proteins