Conclusion:
Quantitation of iTRAQ-labeled peptides in complex mixtures can be successfully performed using HCD fragmentation. In this study, more than 500 proteins from A549 cell lysates were identified and quantified using iTRAQ labeling and an LTQ Orbitrap XL mass spectrometer equipped with an HCD collision cell. Phosphoprotein purification using the Thermo Scientific Phosphoprotein Enrichment Kit increased sample diversity by adding 145 additional proteins. After sequential IMACpurification of a 15 ìg digested PE sample, an additional thirty phosphorylation sites were identified and quantified.

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