The high-throughput identification and accurate quantification of proteins are essential strategies for exploring cellular functions and processes in quantitative proteomics. Stable isotope tagging is a key technique in quantitative proteomic research, accompanied by automated tandem mass spectrometry. For the differential proteome analysis of mouse neuronal cell lines, we used a multiplexed isobaric tagging method, in which a four-plex set of amine-reactive isobaric tags are available for peptide derivatization. Using the four-plex set of isobaric tag for relative and absolute quantitation (iTRAQ) reagents, we analyzed the differential proteome in several stroke time pathways (0, 4, and 8 h) after the mouse neuronal cells have been stressed using a glutamate oxidant. In order to obtain a list of the differentially expressed proteins, we selected those proteins which had apparently changed significantly during the stress test. With 95% of the peptides showing only a small variation in quantity before and after the test, we obtained a list of eight up-regulated and four down-regulated proteins for the stroke time pathways. To validate the iTRAQ approach, we studied the use of oxidant stresses for mouse neuronal cell samples that have shown differential proteome in several stroke time pathways (0, 4, and 8 h). Results suggest that histone H1 might be the key protein in the oxidative injury caused by glutamate-induced cytotoxicity in HT22 cells.