Hi! I would be really glad if someome could help to find a way to do the pre-processing of my proteomic data.

I have some proteomic data made from TMT10plex labeled samples. It consists in two TMT10plex which needs to be normalized together because there is a huge batch-to-batch variation. In other words, I have these 2 sets of 10 samples that I want to normalize to deal with one set of 20 samples.

Unfortunately, I have no internal standard or reference samples, and it's not possible to do the experiment again,

Have you got an idea of a method to eliminate this batch-to-batch variation? I've heard of scalar normalization methods, to normalize to a total sum or the median of each sample, but I am not sure that it could applied here.

Thanks in advance for your help, I am really stuck!

The best,

Robin.