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TaqMan® Protein Assays is a novel technology that uses Proximity Ligation Assay (PLA™) and qPCR for the detection and quantification of proteins in a homogeneous format. PLA is a three-step process that involves, 1) binding of paired antibody-oligonucleotide probes to a protein target in biological samples, 2) ligation of the oligonucleotides, and 3) qPCR detection. This technique has been optimized to create a highly sensitive and specific process for measuring protein expression in small samples. TaqMan® Protein Assays are amenable to many different applications and sample types. TaqMan® Protein Assays have been developed for the pluripotent markers OCT4, NANOG, SOX2, and LIN28 in human stem cells, as well as for over 40 additional human protein targets. Samples as diverse as cell lysates, fixed tissue and whole cells have been successfully used. In addition to detection and quantification, we have developed TaqMan® Protein Assays to monitor protein-protein interactions as well as protein cleavage/activation. Because of the specificity, sensitivity and small sample requirement, TaqMan® Protein Assays are an appealing alternative to more cumbersome and less quantitative methods for protein detection such as western blotting, immunohistochemistry and co-immunoprecipitation. Furthermore, the TaqMan® Protein Assays have been used in conjunction with TaqMan® gene expression and miRNA assays, enabling an integrated qPCR approach to monitor relative changes in mRNA, miRNA and protein from the same starting sample and the same analytical platform.