What is CyTOF?
CyTOF (cytometry by time-of-flight) is a form of mass cytometry used to quantify many protein markers per cell in a single experiment. Antibodies are tagged with metal isotopes, cells are ionized, and a time-of-flight mass analyzer detects the metal signals. This produces high-parameter, single-cell measurements that support deep immune profiling, rare population detection, and robust cohort comparisons.
In practice, CyTOF is widely used in immuno-oncology, infectious disease, inflammation, cell therapy, and systems immunology, where multi-marker signatures are often more informative than any single marker.
Therapeutic Areas
CyTOF is used across research and translational settings where immune systems are complex, multi-dimensional, and clinically meaningful.
Immuno-oncology & Immunotherapy
Use CyTOF to resolve immune context, treatment-induced remodeling, and functional states with enough granularity to detect subtle shifts in activation, exhaustion, and cytotoxic programs. This supports both biomarker discovery and hypothesis-driven evaluation of mechanisms of response and resistance.
Typical groupings:
responder/non-responder · baseline/on-treatment · arm A/arm B
Infectious Disease & Vaccine Response
Quantify immune remodeling across infection, convalescence, or vaccination by combining compositional changes with marker-level shifts. CyTOF is particularly useful when signals are distributed across many markers and rare cell types contribute to protection or pathology.
Typical groupings:
time points · protected/non-protected · acute/convalescent
Autoimmune & Inflammatory Disease
Dissect heterogeneity in immune phenotypes across disease states by mapping multiple functional axes within relevant cell subsets. CyTOF can surface multi-marker signatures that are hard to capture with smaller panels and support stratification for downstream analyses.
Typical groupings:
flare/remission · treated/untreated · phenotype subtypes
Cell Therapy & Functional State Profiling
Assess potency-related phenotypes and functional marker profiles across products, lots, and dosing conditions. CyTOF helps connect manufacturing variation and process parameters to downstream immune state and potential efficacy or safety signals.
Typical groupings:
dose levels · product lots · outcome groups
Typical Study Patterns
Binary Comparisons
Responder vs non-responder, case vs control, treated vs untreated. A common design for prioritizing markers and cell subsets that best separate two cohorts.
Stratification by Metadata
Layer in columns such as age bands, prior therapy, batch, or site. Use stratification to check robustness, identify confounding, and evaluate interaction effects.
Multi-class Studies
Three or more groups, such as multiple arms or phenotype classes. Designed for global tests plus follow-up pairwise comparisons when differences emerge.
Time Point Studies
Baseline, on-treatment, and follow-up comparisons to quantify immune shifts over time, aligned to dosing, progression, or clinical milestones.