GdClean

GdClean removes Gadolinium (Gd) contamination from mass cytometry (CyTOF) datasets to distinguish contaminant Gd-isotope signals from true Gd-isotope-conjugated antibody signals and improve single-cell data quality.

Key Features:

• Gd isotope characterization: Characterizes signals produced by Gd isotopes, including contamination detected in unstained control samples.
• Collinear intensity relationship: Identifies a collinear intensity relationship across Gd contamination signals.
• Reference-based ratio correction: Computes intensity ratios of detected Gd contamination signals to a reference Gd signal and leverages their correlation with natural abundance ratios of Gd isotopes.
• Single-cell decontamination: Distinguishes and removes contaminant signals at the single-cell level while preserving true Gd-labeled antibody signals.
• CyTOF Gd-channel focus: Targets Gd channels affected by Gd-based contrast agents (GBCAs) in mass cytometry data.

Scientific Applications:

• CyTOF data preprocessing: Preprocesses mass cytometry datasets to remove Gd contamination from Gd channels prior to downstream analysis.
• Single-cell biomarker quantification: Improves accuracy of single-cell expression measurements for studies using Gd-labeled antibodies.
• Integration of imaging-exposed samples: Enables analysis of samples exposed to Gd-based contrast agents (GBCAs) alongside standard CyTOF workflows.
• Data quality improvement: Enhances quality control for basic and translational single-cell research involving mass cytometry.

Methodology:

Characterizes Gd isotope contamination signals, identifies collinear intensity relationships among contamination channels, computes intensity ratios to a reference Gd signal, and uses the correlation with natural abundance ratios of Gd isotopes to separate and remove contaminant signals at the single-cell level.