Plants have the ability to memorize past stress events and prime their response more strongly and quickly to cope with recurrent stress. Stress memory is stored in the form of primed confirmation of proteins besides epigenetic and transcriptional regulation of specific hormonal and metabolic signatures. In the past two decades, mass spectrometry-based comparative protein quantification has become a widely used method for understanding the functional role of proteins in perturbation. Isobaric tags for relative and absolute quantification (iTRAQ) is a widely used proteomic technique for the quantification of proteins from multiple samples in a single run. This chapter describes the detailed protocol, including protein isolation, peptide labeling, protein fractionation, LC-MS/MS, and data analysis. We also discussed the application of iTRAQ for plant proteomics in general.