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*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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).

Original languageEnglish
Article number101697
JournalSTAR Protocols
Volume3
Issue number4
DOIs
Publication statusPublished - Dec 2022

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© 2022 The Author(s)

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