Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. II. Limitations of complex mixture analyses

Proteomics. 2001 Jan;1(1):108-17. doi: 10.1002/1615-9861(200101)1:1<108::AID-PROT108>3.0.CO;2-5.


With an emphasis on obtaining a multitude of high quality tandem mass spectrometry spectra for protein identification, instrumental parameters are described for the liquid chromatography-tandem mass spectrometry analysis of trypsin digested unfractionated urine using a hybrid quadrupole-time-of-flight (Q-TOF) mass spectrometer. Precursor acquisition rates of up to 20 distinct precursors/minute in a single analysis were obtained through the use of parallel precursor selection (four precursors/survey period) and variable collision induced dissociation integration time (1 to 6 periods summed). Maximal exploitation of the gas phase fractionated ions was obtained through the use of narrow survey scans and iterative data-dependent analyses incorporating dynamic exclusion. The impact on data fidelity as a product of data-dependent selection of precursor ions from a dynamically excluded field is discussed with regards to sample complexity, precursor selection rates, survey scan range and facile chemical modifications. Operational and post-analysis strategies are presented to restore data confidence and reconcile the greatest number of matched spectra.

MeSH terms

  • Amino Acid Sequence
  • Chromatography, Liquid / methods*
  • Humans
  • Mass Spectrometry / methods*
  • Molecular Sequence Data
  • Peptide Fragments / genetics
  • Peptide Fragments / isolation & purification
  • Proteome / genetics
  • Proteome / isolation & purification*
  • Urine / chemistry


  • Peptide Fragments
  • Proteome