Channel crosstalk correction in suspension and imaging mass cytometry

Mass cytometry enables simultaneous analysis of over 40 proteins and their modifications in single cells through use of metal-tagged antibodies. Compared to fluorescent dyes, the use of pure metal isotopes strongly reduces spectral overlap among measurement channels. Crosstalk still exists, however, caused by isotopic impurity, oxide formation, and mass cytometer properties. Spillover effects can be minimized, but not avoided, by following a set of constraining rules when designing an antibody panel. Generation of such low crosstalk panels requires considerable expert knowledge, knowledge of the abundance of each marker and substantial experimental effort. Here we describe a novel bead-based compensation workflow that includes R-based software and a web tool, which enables correction for interference between channels. We demonstrate utility in suspension mass cytometry and show how this approach can be applied to imaging mass cytometry. Our approach greatly simplifies the development of new antibody panels, increases flexibility for antibody-metal pairing, improves overall data quality, thereby reducing the risk of reporting cell phenotype and function artifacts, and greatly facilitates analysis of complex samples for which antigen abundances are unknown.