Heilongjiang University of Chinese Medicine 1 article published in JoVE Biochemistry Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification Anthony A. High1, Haiyan Tan1, Vishwajeeth R. Pagala1, Mingming Niu2,3, Ji-Hoon Cho1, Xusheng Wang1, Bing Bai2, Junmin Peng1,2 1 We present a protocol to accurately quantitate proteins with isobaric labelling, extensive fractionation, bioinformatics tools, and quality control steps in combination with liquid chromatography interfaced to a high-resolution mass spectrometer.