Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline

Paulina Rybakowska; Sofie Van Gassen; Jordi Martorell Marugán; Katrien Quintelier; Yvan Saeys; Marta E Alarcón-Riquelme; Concepción Marañón

doi:10.1016/j.xpro.2022.101697

Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline

STAR Protoc. 2022 Oct 31;3(4):101697. doi: 10.1016/j.xpro.2022.101697. eCollection 2022 Dec 16.

Authors

Paulina Rybakowska¹, Sofie Van Gassen², Jordi Martorell Marugán³, Katrien Quintelier⁴, Yvan Saeys², Marta E Alarcón-Riquelme⁵, Concepción Marañón⁶

Affiliations

¹ GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/ Andalusian Regional Government, PTS, 18016 Granada, Spain. Electronic address: paulina.rybakowska@genyo.es.
² Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, 9000 Gent, Belgium; Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9000 Gent, Belgium.
³ GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/ Andalusian Regional Government, PTS, 18016 Granada, Spain; Department of Statistics and Operational Research, University of Granada, 18071 Granada, Spain; Data Science for Health Research Unit, Fondazione Bruno Kessler, 38123 Trento, Italy.
⁴ Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, 9000 Gent, Belgium; Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9000 Gent, Belgium; Department of Pulmonary Diseases, Erasmus MC, 3015 Rotterdam, the Netherlands.
⁵ GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/ Andalusian Regional Government, PTS, 18016 Granada, Spain; Institute for Environmental Medicine, Karolinska Institute, 17177 Stockholm, Sweden.
⁶ GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/ Andalusian Regional Government, PTS, 18016 Granada, Spain. Electronic address: concepcion.maranon@genyo.es.

Abstract

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 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).

Keywords: Clinical protocol; Flow cytometry/Mass cytometry; Immunology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Flow Cytometry / methods
Leukocytes, Mononuclear*
Monitoring, Immunologic
Multicenter Studies as Topic
Reproducibility of Results
Retrospective Studies