Handling values <LOD for protein intensities

Question

[mdhale121]

Hello All,

I am not sure if this forum is the right place to ask questions related handling protein intensities values but I would really appreciate any help that I can get.

So our lab quantified a few proteins using the Quanterix platform for a longitudinal study we are working on. The data looks fine overall but there are few values which are annotated as less than LOD, what is the best way to handle these values. Can I substitute them to zero or should I just drop the sample?

Answer 1

[pbpanigrahi]

If a given protein is below LOD, limit of detection, across more than x% sample, then you can ignore. X depends on your field of study. If lets say you want to ignore a protein if it is absent/below LOD for more than 5% sample, then you ignore them. If you want to keep them, then either substitute with zero or the minimum value. Depending upon the data, you need to normalize them so that samples and proteins are comparable.