Hybridization of pulsed-Q dissociation and collision-activated dissociation in linear ion trap mass spectrometer for iTRAQ quantitation.
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.
Guo
Tiannan
T
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, and Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610.
Gan
Chee Sian
CS
Zhang
Huoming
H
Zhu
Yi
Y
Kon
Oi Lian
OL
Sze
Siu Kwan
SK
D000465:Algorithms; D000818:Animals; D002364:Caseins / Q000378:metabolism; D002417:Cattle; D045744:Cell Line, Tumor; D002645:Chickens; D019295:Computational Biology / Q000379:methods; D045304:Cytochromes c / Q000378:metabolism; D006736:Horses; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D009113:Muramidase / Q000378:metabolism; D009211:Myoglobin / Q000378:metabolism; D010047:Ovalbumin / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012680:Sensitivity and Specificity; D012710:Serum Albumin, Bovine / Q000378:metabolism; D013274:Stomach Neoplasms / Q000378:metabolism / Q000473:pathology
D002364:Caseins; D009211:Myoglobin; D012710:Serum Albumin, Bovine; D010047:Ovalbumin; D045304:Cytochromes c; C421864:hen egg lysozyme; D009113:Muramidase