Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline Rybakowska, Paulina Martorell Marugán, Jordi Alarcón Riquelme, Marta Eugenia Marañón Lizana, Concepción Support has been received (PI: M.E.A.) from the IMI2-JU project GA No 831434 (3TR) and IMI-JU project GA No 115565 (PRECISESADS). P.R. has received support from EMBO (7966) and from Consejería de Salud de Junta de Andalucía (EF-0091-2018). C.M. acknowledges funding from Programa Nicolas Monardes (C2-0002-2019). J.M.M. is funded by European Union-NextGenerationEU, Ministry of Universities (Spain’s Government) and the Recovery, Transformation and Resilience Plan. These results form a part of the P.R. PhD thesis in Biomedicine at the University of Granada. We are grateful to Olivia Santiago and Jose Diaz Cuéllar for technical support as a Core facility in Genyo research center. Also, we would like to express our gratitude to the donors. The figures in this paper were created with BioRender.com Mass cytometry (MC) is a powerful large-scale immune monitoring technology. To maximize MC data quality, we present a protocol for whole blood analysis together with an R package, Cyto Quality Pipeline (CytoQP), which minimizes the experimental artifacts and batch effects to ensure data reproducibility. We describe the steps to stimulate, fix, and freeze blood samples before acquisition to make them suitable for retrospective studies. We then detail the use of bar-coding and reference samples to facilitate multicenter and multi-batch experiments.For complete details on the use and execution of this protocol, please refer to Rybakowska et al. (2021a) and (2021b). 2023-10-25T10:23:03Z 2023-10-25T10:23:03Z 2022-12-16 journal article Rybakowska P. et al. Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline. STAR Protocols 3, 4, 101697. [https://doi.org/10.1016/j.xpro.2022.101697] https://hdl.handle.net/10481/85242 10.1016/j.xpro.2022.101697 eng http://creativecommons.org/licenses/by-nc-nd/4.0/ open access Attribution-NonCommercial-NoDerivatives 4.0 Internacional Elsevier