Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology


An isotope tags for relative and absolute quantitation (iTRAQ)-based reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) method was developed for differential protein expression profiling in complex cellular extracts. The estrogen positive MCF-7 cell line, cultured in the presence of 17β-estradiol (E2) and tamoxifen (Tam), was used as a model system. MS analysis was performed with a linear trap quadrupole (LTQ) instrument operated by using pulsed Q dissociation (PQD) detection. Optimization experiments were conducted to maximize the iTRAQ labeling efficiency and the number of quantified proteins. MS data filtering criteria were chosen to result in a false positive identification rate of <4%. The reproducibility of protein identifications was ∼60%–67% between duplicate, and ∼50% among triplicate LC-MS/MS runs, respectively. The run-to-run reproducibility, in terms of relative standard deviations (RSD) of global mean iTRAQ ratios, was better than 10%. The quantitation accuracy improved with the number of peptides used for protein identification. From a total of 530 identified proteins (P < 0.001) in the E2/Tam treated MCF-7 cells, a list of 255 proteins (quantified by at least two peptides) was generated for differential expression analysis. A method was developed for the selection, normalization, and statistical evaluation of such datasets. An approximate ∼2-fold change in protein expression levels was necessary for a protein to be selected as a biomarker candidate. According to this data processing strategy, ∼16 proteins involved in biological processes such as apoptosis, RNA processing/metabolism, DNA replication/transcription/repair, cell proliferation and metastasis, were found to be up- or down-regulated.


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Correspondence to Iulia M. Lazar.

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Published online March 4, 2009

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Armenta, J.M., Hoeschele, I. & Lazar, I.M. Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology. J Am Soc Mass Spectrom 20, 1287–1302 (2009). https://doi.org/10.1016/j.jasms.2009.02.029

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  • Tandem Mass Spectrum
  • Relative Standard Deviation
  • iTRAQ Reagent
  • iTRAQ Ratio
  • Linear Trap Quadrupole