Mass Cytometry: Vaporizing Cells in the Name of Science

May 6, 2011 at 5:13 pm 6 comments

Mass cytometry, a technique developed by DVS Sciences, now a Fluidigm Company represents a revolutionary spin on classic fluorescence-based flow cytometry. Instead of using antibodies tagged with fluorophores (in which spectral overlap quickly limits the number of parameters available for simultaneous detection), mass cytometry relies on antibodies tagged with transition element isotopes. Antibody-bound cells are vaporized, ionized, and analyzed on a mass spectrometer.

In a paper published today in Science, Garry Nolan’s lab at Stanford University (website, Public Cytometry Collection), in collaboration with DVS Sciences, now a Fluidigm Company reports the use of this technology to examine human bone marrow samples. The team simultaneously measured 34 cellular parameters in each single cell – including 13 surface markers and 18 intracellular epitopes. Their data set provides information on all the various cell types present in bone marrow, as well as information about the signaling of these cells in response to perturbation.

Cytobank is excited to host the data from this study, facilitating both viewing and deeper mining of the high-dimensional data set. Access the data by going to the Nolan Lab’s Public Cytometry Collection and clicking “View Data” for the Science paper. Anyone can view the Cytobank Report for the paper (learn more about Cytobank Reports), but you will need an account on Cytobank in order to access the data (register for free).

Bone marrow is a complex heterogeneous tissue consisting of cells ranging in developmental stage from hematopoietic stem cells to highly specialized subsets of immune cells. These cell types can be characterized by their expression of specific surface markers. Using a novel method called spanning-tree progression analysis of density-normalized events (SPADE), the authors analyzed their surface marker data set and visualized it as tree plots representing the developmental progression in bone marrow, with each branch representing different cell lineages and each node representing an immunological cell population.

Overlaying signaling behavior on the tree structure enabled the authors to identify and visualize signaling responses specific to certain cell types and lineages. Known specific signaling responses – IL-7 induced p-STAT5 phosphorylation in T cells, for example – were confirmed to validate the approach. The team then examined previously unidentified and unexpected signaling behaviors, including gradual changes in signaling observed across a continuum of developing cells. Notably, they also examined change in signaling behavior resulting from treatment with kinase inhibitors. Analysis of healthy bone marrow treated with dasatinib, a kinase inhibitor used to treat patients with chronic myelogenous leukemia, revealed off-target activity that may have both beneficial and harmful consequences for patients.

The findings reported in the paper demonstrate how mass cytometry data can provide a systems-level view of the immune system during healthy development, as well as in disease states and after drug therapy.

To learn more about the study, read the Perspective article also published in Science and a news article from the Stanford School of Medicine.

– Stephanie


Bendall SC, Simonds EF, Qiu P, Amir ED, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe’er D, Tanner SD, Nolan GP. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011 May 6; 332(6030):687-96. Abstract.

Entry filed under: Flow Cytometry. Tags: , , , , , , , .

Cytometry in the Cloud A New Way to Publish Data: Cytobank Reports

6 Comments Add your own

  • […] mass cytometry study (read our take on it here) demonstrates other reasons why a resource like Cytobank Reports is necessary. Both the size of the […]

  • […] SPADE (which stands for spanning-tree progression analysis of density-normalized events) is a way to automatically identify populations in multidimensional flow cytometry data files. SPADE clusters cells into populations and then projects them into a tree like the one shown above. SPADE works for data from both ‘classic’ fluorescence flow cytometry and mass cytometry. […]

  • […] more than 30 different flow cytometer models, so chances are that Cytobank can handle your data! In a recent post, we featured the ability of Cytobank to facilitate the mining of data from large datasets generated […]

  • […] Reports. You can see Cytobank Reports in action by viewing the Report created for the Nolan Lab’s recent mass cytometry study. Cytobank Reports also powers the datasheets in the BD FACSelect Buffer Compatibility Resource. In […]

  • […] Mass Cytometry: Vaporizing Cells in the Name of Science – Learn about mass cytometry, where antibodies are conjugated to element isotopes instead of fluorphores, increasing the number of cellular parameters that can be assayed in one sample tube. Access the raw data from a Nolan lab dataset published in Science this year, and try your hand at analyzing mass cytometry data yourself! […]

  • […] trend towards high dimensional flow cytometry, including mass cytometry, allows scientists to assess increasing numbers of targets simultaneously. This means that gating […]


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