Mass Cytometry Dataset for "Mass cytometry discloses heterogeneity of immune cell proteases"
Description
This dataset supports the manuscript “Mass cytometry discloses heterogeneity of immune cell proteases,” accepted in Cell Reports. The research hypothesis driving the study was that innate immune cells, particularly neutrophils and macrophages, exhibit previously unrecognized heterogeneity in their protease activity profiles, and that this heterogeneity can be detected using activity-based TOF probes and mass cytometry. The dataset consists of raw CyTOF FCS files generated from primary human neutrophils and THP-1 monocytes differentiated into M0, M1, and M2 macrophages. Cells were labeled with either cysteine-reactive or serine-reactive TOF probes designed to detect active proteases within each cell population. Control probe samples lacking the reactive warhead are also included (denoted with “C” in the filenames). Following probe labeling, cells were fixed and stained with a panel of metal-tagged antibodies specific for immune cell proteases to enable simultaneous detection of active enzymes and total protease abundance. This dataset allows users to examine raw single-cell protease activity signatures across different innate immune cell states. Although gating, normalization, and downstream analyses were performed in Cytobank for the published manuscript, the raw FCS files provided here can be re-gated or re-analyzed using any CyTOF-compatible software. A metal tag map is included to clarify which antibodies and probes correspond to each metal isotope. All experimental procedures including cell preparation, probe labeling, fixation, metal-antibody staining, and CyTOF acquisition, are described in the STAR Methods of the associated manuscript, enabling full reproducibility. This dataset provides a resource for researchers interested in protease biology, innate immune heterogeneity, activity-based probes, and single-cell mass cytometry.
Files
Steps to reproduce
The raw mass cytometry (CyTOF) data in this dataset were generated from primary human neutrophils and THP-1 monocytes differentiated into M0, M1, or M2 macrophages. Cells were prepared, stimulated, and processed exactly as described in the Methods section of the associated Cell Reports manuscript. For probe labeling, cells were incubated with cysteine-reactive or serine-reactive TOF probes. Control samples lacking the reactive warhead were processed in parallel. Following fixation, cells were stained with a panel of metal-labeled antibodies targeting proteases of interest. This repository includes the raw FCS files and a metal tag map indicating which antibodies and probes correspond to which metal isotopes. All experimental details required to fully reproduce the sample preparation, probe labeling, antibody staining, and CyTOF acquisition procedures are provided in the published manuscript’s detailed STAR Methods. No gating, preprocessing, or downstream analyses are included here; these steps were performed in Cytobank and are available upon request.
Institutions
- Sanford Burnham Prebys Medical Discovery Institute