Immune Monitoring Virtual Course 2020

Welcome to the Maecker Lab Online Course on Mass Cytometry (CyTOF)!

This course is designed to teach you about the CyTOF instrument, possible assays, and analysis techniques, from basic to advanced.  It is designed as a series of linked resources, including videos, slide presentations, web tutorials, and readings.  These are organized under the major topic headings below.  The links under each topic are organized for sequential viewing from top to bottom, with additional resources listed at the end.  Of course, you can choose to skip to particular topics of interest as you like.  We link to a number of external sources, and we thank all those who contributed material for this course (acknowledged on the topic pages).  Please address any feedback, questions, or issues with weblinks to Mina Pichavant.

Mass cytometry, or CyTOF (for Cytometry by Time of Flight) is a highly multiparameter version of flow cytometry, in which the reporter molecules are heavy metal ions, read on a single-cell basis by mass spectrometry, rather than fluorophores read by laser excitation and fluorescence emission.  The main benefit of CyTOF is an ability to combine 45+ antibodies or other reporters, with much reduced spillover between detector channels, relative to fluorescence flow cytometry.  Similar assays can be performed as in fluorescence flow cytometry, albeit at lower cell collection speeds.  Data analysis is more challenging due to the complexity of the data, and is aided by the development of automated clustering and visualization algorithms for high-dimensional single-cell data.

General Resources:

•       A quick comparison of flow and mass cytometry for beginners. (Harari, Journal of Immunotherapy of Cancer, 2015)

•       Web tutorials for cytometrists and data scientists on all aspects of CyTOF data

•       The Stanford CytoForum is an online forum covering all aspects of CyTOF.

Part 1.  Instrumentation and Reagent Generation

This page introduces the CyTOF platform, and provides resources on instrument setup, antibody conjugation, and optimal panel design for CyTOF.

Part 2.  CyTOF Assays

This page provides resources on basic assay types as practiced in the Maecker lab, including immunophenotyping, intracellular cytokine staining, and phospho-signaling.

Part 3.  Data Analysis

This page links to resources on manual gating in FlowJo or Cytobank, and descriptions of automated analysis algorithms, as well as public data repositories.


Continue to Part 1. Instrumentation and Reagent Generation...

Important Dates:

Wednesday September 16th 2020: Introduction course

Please send out your questions through this Survey link:

Monday September 21st, 2020 at 10 am PT: Q&A on Instrumentation & Reagent Generation and CyTOF Assays

Friday September 25th, 2020 at 10 am PT: Q&A on Data Analysis

Please contact Mina Pichavant if you have not received the invite.