PFCC Mass Cytometry Training

Hands-on CyTOF Training

Overview: All CyTOF users need to fulfill Basic Training requirements, which covers Core logistics, mass cytometry basics, experimental design, instrument utilization, workflow, CyTOF software overview, running test samples, system changeover/shutdown, analysis options, data management, and general troubleshooting.

The type of training conducted is dependent on your needs.  If you plan to run during normal working hours (Monday-Friday from 8am-5pm), Basic Training will suffice.  Members of the Flow Core perform "CyTOF-Setup" during normal working hours based off the scheduled users.  If you plan to run samples heavily during nights, weekends, and holidays, you should take Advanced Training also.  The Core will provide all necessary reagents and samples for the Hands-On training.  For the Guidance sessions, you will provide your own samples.  If you run samples infrequently and feel that it is not worth learning how to use the CyTOF, it is recommended to request Assistance to have a Flow Core Staff member run samples for you.

Resources:  Please view the manual before your scheduled training, as it will help you in understanding mass cytometry basics (Chapter 1, pages 4-21) and the software (Chapter 5, pages 94-101). 

1)  Recommended for new users of the CyTOF:  Helios User Guide V6.7  

2)  Get an account here as this will give you access to important resources and background info as well as the panel designer: 

3)  See here for product support including the link for the Fluidigm Debarcoder software:

4)  See here for the link to the Nolan lab tools such as their debarcoder and normalization programs:

Basic Training Requirements:  We allow you to evaluate your skill level (Novice, Experienced), but if we observe you need additional help, you will be required to take supplementary training.  Choose from one of the 2 options:

  • Novice Training: is done on individual level and consists in performing a pilot experiment with your panel. You will learn how to stain (link to protocol), barcode and run your stained samples on the available Helios. Please email the staff at [email protected] and ask about training availability.
  • Experienced user: If you are a New User please sign up for the Onboarding Session at PFCC.


Hands-on MIBIscope Training

(details coming soon)

Advanced Mass Cytometry Training options

CyTOF SuperUser
Antibody Conjugation Training - CyTOF
Antibody Conjugation Training - MIBI

(details coming soon)