Rybakowska, PaulinaVan Gassen, SofieMartorell Marugán, JordiQuintelier, KatrienSaeys, YvanAlarcón-Riquelme, Marta EMarañón, Concepción2023-05-032023-05-032022-10-31http://hdl.handle.net/10668/22544Mass 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 barcoding 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).enAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/Clinical protocolFlow cytometry/Mass cytometryImmunologyMonitoring, ImmunologicFlow CytometryReproducibility of ResultsRetrospective StudiesLeukocytes, MononuclearMulticenter Studies as Topicresearch article36353363open access10.1016/j.xpro.2022.1016972666-1667PMC9637821https://doi.org/10.1016/j.xpro.2022.101697https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9637821/pdf