Agile workflow for interactive analysis of mass cytometry data

Motivation Single-cell proteomics technologies, such as mass cytometry, have enabled characterization of cell-to-cell variation and cell populations at a single cell resolution. These large amounts of data, however, require dedicated, interactive tools for translating the data into knowledge. Results We present a comprehensive, interactive method called Cyto to streamline analysis of large-scale cytometry data. Cyto is a workflow-based open-source solution that automatizes the use of of state-of-the-art single-cell analysis methods with interactive visualization. We show the utility of Cyto by applying it to mass cytometry data from peripheral blood and high-grade serous ovarian cancer (HGSOC) samples. Our results show that Cyto is able to reliably capture the immune cell sub-populations from peripheral blood as well as cellular compositions of unique immune- and cancer cell subpopulations in HGSOC tumor and ascites samples. Availability The method is available as a Docker container at and the user guide and source code are available at Contact sampsa.hautaniemi{at}helsinki.fi Supplementary information Supplementary material is available and FCS files are hosted at flowrepository.org/id/FR-FCM-Z2LW ### Competing Interest Statement The authors have declared no competing interest.