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Single cell analysis using flow and mass cytometry

The purpose of the course is to prepare and train course participants to plan mass cytometry experiments on a detailed level and to be able to decide which analytical software to use on acquired mass cytometry data.

To attend, the course participants must have experience of multi-parameter flow cytometry.

Important dates

Preliminary date: 15-31 May (weeks 20-22), 2018

Application open: February 15, 2018

Application deadline: April 15, 2018

Confirmation to accepted participants: April 23, 2018

Responsible teacher/s:

Jörgen Adolfsson,

Contact information for questions regarding the course: Therese Pettersson


Jan-Ingvar Jönsson

Course content

Flow cytometry is the method of choice when single cell multiplex analysis of protein receptors are to be examined with fluorochrome labeled antibodies. Unfortunately problems with spectral overlap occur from the different fluorochromes necessitating color compensation. This will in practice restrict experiments to analyzing only 12-16 proteins on a single cell level.

A mass cytometer or Cytometry by Time-Of-Flight (CyTOF), however, has the capacity to analyze up to 40 proteins at a single cell level. This is made possible by utilizing rare earth metals conjugated to antibodies instead of fluorochromes. The different masses of the individual metals are easily detected by the time-of-flight mass spectrometer thus rendering the need for compensation unnecessary.

The course will include lectures concerning:

  • An introduction to single cell analysis at protein level
  • Basic principles in flow cytometry
  • Basic principles in mass cytometry
  • The CyTOF2 instrument
  • How to design a panel of metal tagged antibodies
  • Presentation of different multi-parameter analysis software
  • Introduction on how to use one analysis software
  • A demonstration of the CyTOF2 instrument will be given


Entry requirements

To qualify for studies on third-cycle education courses, you must have a:

  • second-cycle degree, 240 credits in required courses, including at least 60 second-cycle credits, or acquired equivalent knowledge in some other manner

For this course you are also required to have experience of multi-parameter flow cytometry. Priority will be given to those who have a planned and/or on-going mass cytometry project.


Presence at all seminars is required. Participation in discussions will be evaluated

 Course homepage