Why is the expression of my target protein very low in my InTraSeq™ experiment?

Sometimes, doublets and multiplets in single-cell datasets can skew the protein visualization in FeaturePlot. Using a maximum cutoff (max.cutoff) bypasses the observed high level of protein expression from outliers and allows clear visualization. Use a large value for this parameter, such as "q90" or higher ("q95", "q99", etc.) as appropriate for your experiment. See the example in bold below:
 

FeaturePlot(object, features = c("protein_Phospho-S6(Ser235-236)-Ab"), max.cutoff = “q90”, min.cutoff = "q5")

It is also important to read the published literature and mine public databases to ensure that your protein is expressed in your sample, and learn what conditions may change that expression.

If a non-InTraSeq-validated antibody is used, insufficient antibody binding can skew visualization. Use CST® InTraSeq-validated antibodies in your single-cell experiments and follow the InTraSeq protocol precisely to ensure reliable and reproducible results.

Last updated: July 25, 2025