Making it work: lessons learned from setting up Australias first mass cytometry facility

Mass cytometry is a powerful technology, however there are a number of practical challenges that potentially limit its uptake. Some of these challenges are specific to Australia. Here we detail experience gained from the first nine months of operation of the test-case Australian facility, and the approaches we have taken to make mass cytometry available to a broad base of researchers. An important factor limiting the uptake of mass cytometry is the costs involved, in particular that of consumables. In Australia, metal-conjugated antibodies are ~5-10 times more expensive on a per test basis than their fluorochrome-conjugated equivalents. Furthermore, panels are typically large (25-35 parameters). To lower this barrier to entry we have collected a centralised bank of core reagents that researchers can access through a barter or cost-recovery system. We have also assessed the titres and overall cost effectiveness of pre-conjugated vs. in-house conjugated antibodies. Argon usage also adds to CyTOF running costs and we have found these to be significantly higher than estimates provided by other sites worldwide. Cost comparisons between pressurised cylinders and liquid argon Dewars as argon sources are presented. Finally, because of the highly parametric nature of mass cytometric data, it is best analysed by automated approaches. Although integrated analysis packages are available through commercial suppliers, a number of widely used analysis tools are available as open-source, either as Matlab or R packages. Analysis approaches are illustrated using data sets from studies investigating myeloid diversity in the mouse and human.

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