What Are CD1 Capture Scores?
CD1 capture scores in the ImmunoLipid Atlas come directly from the dataset published by Huang et al. who recovered lipid from B2m-linked and unlinked CD1a isoforms (CD1a, CD1b, CD1c, and CD1d) expressed in K562 and 293T cells. The scores are directly related to the average LC-MS signal intensity (peak area) of each recovered lipid species, and thus represent a semi-quantitative measure of how efficiently each CD1 isoform captured a given lipid.Since the readout depends on both biochemical interaction and mass-spectrometric response, capture scores should be interpreted as relative indicators of CD1 binding, not absolute binding affinities. I.e., where a higher score means the more lipid was recovered under the tested assay conditions; a lower or zero score indicates weak or no recovery.
In the ImmunoLipid Atlas, capture scores are represented in the heatmaps, visualizing the how the abundance of a given lipid in those described testing conditions relates to its capture profile by CD1 isoforms.
Reference:
Huang C. et al., Cell (2023)
How Is Lipid Abundance Calculated?
Lipid abundance values shown in the ImmunoLipid Atlas represent the normalized percentage of each lipid species relative to the total lipid signal within a given sample. After LC-MS acquisition, all detected lipids in a sample are therefore summed together, and signal is calculated for each lipid as a percentage of the total lipid content for the given sample. The color scale represents these percentages in the heatmap visualizations, allowing users to quickly assess lipid composition, and compare different modalities.