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

Tiannan Guo, Chee Sian Gan, Huoming Zhang, Yi Zhu, Oi Lian Kon, Siu Kwan Sze

    Research output: Contribution to journalArticlepeer-review

    55 Scopus citations

    Abstract

    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.

    Original languageEnglish (US)
    Pages (from-to)4831-4840
    Number of pages10
    JournalJournal of Proteome Research
    Volume7
    Issue number11
    DOIs
    StatePublished - Nov 1 2008

    Keywords

    • Collision-activated dissociation
    • Gastric cancer
    • Ion trap
    • Pulsed-Q dissociation
    • Quantitative proteomics
    • iTRAQ

    ASJC Scopus subject areas

    • Biochemistry
    • Chemistry(all)

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