Hybridization of pulsed-Q dissociation and collision-activated dissociation in linear ion trap mass spectrometer for iTRAQ quantitation

J Proteome Res. 2008 Nov;7(11):4831-40. doi: 10.1021/pr800403z. Epub 2008 Oct 7.


Coupling of multiplex isobaric tags for relative and absolute quantitation (iTRAQ) to a sensitive linear ion trap (LTQ) mass spectrometer (MS) is a challenging, but highly promising approach for quantitative high-throughput proteomic profiling. Integration of the advantages of pulsed-Q dissociation (PQD) and collision-activated dissociation (CAD) fragmentation methods into a PQD-CAD hybrid mode, together with PQD optimization and data manipulation with a bioinformatics algorithm, resulted in a robust, sensitive and accurate iTRAQ quantitative proteomic workflow. The workflow was superior to the default PQD setting when profiling the proteome of a gastric cancer cell line, SNU5. Taken together, we established an optimized PQD-CAD hybrid workflow in LTQ-MS for iTRAQ quantitative proteomic profiling that may have wide applications in biological and biomedical research.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Caseins / metabolism
  • Cattle
  • Cell Line, Tumor
  • Chickens
  • Computational Biology / methods
  • Cytochromes c / metabolism
  • Horses
  • Humans
  • Mass Spectrometry / methods*
  • Muramidase / metabolism
  • Myoglobin / metabolism
  • Ovalbumin / metabolism
  • Proteomics / methods*
  • Sensitivity and Specificity
  • Serum Albumin, Bovine / metabolism
  • Stomach Neoplasms / metabolism
  • Stomach Neoplasms / pathology


  • Caseins
  • Myoglobin
  • Serum Albumin, Bovine
  • Ovalbumin
  • Cytochromes c
  • hen egg lysozyme
  • Muramidase