Rybakowska, PaulinaVan Gassen, SofieQuintelier, KatrienSaeys, YvanAlarcón-Riquelme, Marta E.Marañón, Concepción2022-11-182022-11-182021-05-21Rybakowska P, Van Gassen S, Quintelier K, Saeys Y, Alarcón-Riquelme ME, Marañón C. Data processing workflow for large-scale immune monitoring studies by mass cytometry. Comput Struct Biotechnol J. 2021 May 21;19:3160-3175http://hdl.handle.net/10668/4361Mass cytometry is a powerful tool for deep immune monitoring studies. To ensure maximal data quality, a careful experimental and analytical design is required. However even in well-controlled experiments variability caused by either operator or instrument can introduce artifacts that need to be corrected or removed from the data. Here we present a data processing pipeline which ensures the minimization of experimental artifacts and batch effects, while improving data quality. Data preprocessing and quality controls are carried out using an R pipeline and packages like CATALYST for bead-normalization and debarcoding, flowAI and flowCut for signal anomaly cleaning, AOF for files quality control, flowClean and flowDensity for gating, CytoNorm for batch normalization and FlowSOM and UMAP for data exploration. As proper experimental design is key in obtaining good quality events, we also include the sample processing protocol used to generate the data. Both, analysis and experimental pipelines are easy to scale-up, thus the workflow presented here is particularly suitable for large-scale, multicenter, multibatch and retrospective studies.enAttribution-NonCommercial-NoDerivatives 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-nd/4.0/Mass cytometrySemi-automated data preprocessingImmune phenotypingData normalizationQuality controlWorkflowArtifactsFlow cytometryControl de calidadFlujo de trabajoArtefactosCitometría de FlujoMonitorización inmunológicaInmunofenotipificaciónMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Epidemiologic Studies::Case-Control Studies::Retrospective StudiesMedical Subject Headings::Information Science::Information Science::Systems Analysis::WorkflowMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Monitoring, Physiologic::Monitoring, ImmunologicMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::ArtifactsMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Methods::Research DesignMedical Subject Headings::Technology and Food and Beverages::Technology, Industry, and Agriculture::Technology::Quality ControlMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Clinical Laboratory Techniques::Specimen HandlingMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Clinical Trials as Topic::Multicenter Studies as TopicMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Immunologic Techniques::Immunologic Tests::Immunophenotypingresearch article34141137Acceso abierto10.1016/j.csbj.2021.05.0322001-0370PMC8188119