University of Minnesota
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Mass Cytometry News, Activities and Training

Upcoming Activities and Training Related to Mass Cytometry:

What is Mass Cytometry?

Similar to flow cytometry, which uses fluorescently labeled antibodies to tag molecular targets in cells, mass cytometry uses antibodies tagged with stable metal isotopes. Each antibody used has a unique metal tag. The instrument allows for collection of one mass spectrum per cell. Each mass spectrum includes ions for the metal tags present in the cell that originated the spectrum. Each ion signature indicates the abundance of the corresponding molecular target. The resulting data sets contain up to 34 parameters per cell, which provides the most comprehensive description of heterogeneity at the single cell level. This technique has been used to study cellular senescence, or degradation, as well as different response to drug treatments. A few select references are available here.

Sachs, et al; Blood 2014

Image courtesy of Zohar Sachs; showing SPADE trees of untreated (left) and treated (right) cell populations. Circle sizes represent the size of the cell populations matching a specific protein profile, colors indicate signal intensity for the evaluated protein marker for that rendering. Click here to see the figure rendered for two different markers.

Instrumentation and Access

The current mass cytometer (CyTOF2) is installed at the Mass Spectrometry Laboratory, Department of Chemistry, University of Minnesota. Technical details on this technology are available at this site.

User Incentives

Rates: $30/hour (for U of M and Mayo researchers). For other rates click here. Schedule: To set up an account send fill out this account form - be sure to check the box "720404 (Scientific Services)" - then send it as a PDF in an email to Joe Dalluge. To view the schedule click here.

Mass Cytometry Work Flow

Contact Heather Grundhofer for help.

  1. Select metal tags for each antibody. Do on your (Fluidigm tool, registration required) own or contact us
  2. Purchase metal-tagged antibodies from Fluidigm, our metal-tagged antibody library (see below). You may also purchase non-tagged antibodies and we will train you on the process of metal tagging.
  3. Test your antibody panel with your sample. Prepare your samples and run them in the CyTOF2. Antibodies can be tested at the same time as long as they have different metal tag. We can provide protocols. For instrument usage and training contact Sean Murray.
  4. Select optimal concentrations of antibody. Titration experiment.
  5. Conduct your CyTOF measurements using optimized antibody concentrations.
  6. Analyze your data using SPADE or ViSNE using CytoBank. We can provide access to the software.

Metal-tagged Antibody Library

We have an antibody library that includes metal-tagged antibodies from Fluidigm. Download the current list here. Researchers can purchase small aliquots of each antibody (~ $3-6/aliquot) sufficient to label 3-6 million cells. This reduces significantly the antibody cost (For instance, to label 2 samples with 10 different antibodies will cost ~ $90; running the samples for 30 minutes each will cost in total ~ $30).

To access the current list of reagents and antibodies click here

For PI's only: Done only once. To approve the purchase of antibodies by your research group send an e-mail to Edgar Arriaga with the following information: (1) List of people approved to purchase antibodies, (2) EFS string. (3) Justification for accounting purposes.


Fluidigm. The manufacturer maintains educational and training material, catalogue of reagents and supplies for mass cytometry, literature, and resources for data analysis. This company frequently organizes workshops on campus and provide consultation to users.

CytoForum. This user group is maintained by researchers at Stanford University. It is a great resource to exchange ideas and post questions to other user. Registration is free and required to post questions/comments.

Flow Cytometry Resource. Flow cytometry is a commonly used method to assess suitability of new antibodies destined for metal tagging for mass cytometric analysis. This facility is available to all users for a fee.

University Imaging Centers. Immunoimaging is another method that could be used to assess the suitability of new antibodies destined for metal tagging for mass cytometric analysis. This facility is available to all users for a fee.

Minnesota Supercomputing Institute. The MSI provides access to BioLearn and SPADE analytical modules (for R) on the lab cluster thus providing users with command line options for mass cytometer data analysis. Access to the software requires the user to hold an active MSI account. To request an account please follow the procedures described at: MSI account signup.

Other Mass Cytometry Resources. We maintain educational materials such as archived presentations. To loan these resources, contact Heather Grundhofer.

Steering Committee Members

At the University of Minnesota: Edgar A. Arriaga, Joshua Baller, Paul Champoux, Joseph Dalluge, Marc Jenkins, Brian Fife, Dan Kaufman, Wei-Shou Hu, Zohar Sachs.

At Mayo Clinic: James Kirkland, Jeff Salisbury, Guo Yi

Funding Sources

Purchase and installation of the instrumentation: Office of the Vice President for Research, College of Science and Engineering, Department of Chemistry, Medical School.

Recruitment, training, and adaptation into research programs: Minnesota Partnership for Biotechnology and Medical Genomics, Office of the Vice President for Research, Medical School, Center for Immunology, Stem Cell Institute