The described protocol provides an optimized quantitative proteomics analysis of tissue samples using two approaches: label-based and label free quantitation. Label-based approaches have the advantage of more accurate quantitation of proteins, while a label-free approach is more cost-effective and used to analyze hundreds of samples of a cohort.
Verma, A., Kumar, V., Ghantasala, S., Mukherjee, S., Srivastava, S. Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples. J. Vis. Exp. (177), e61786, doi:10.3791/61786 (2021).