Normalisation at the peptide level

[JesseIL]

Hi, I'm processing a peptidomics data set and was wondering if, when I select 'normalise data', does it normalise only the protein intensities or the peptide intensities too? Does it do it for each biological group separately? Thanks,

Yishai

[rmillikin]

Hi Yishai,

Normalization occurs on the peptide level, and then that indirectly carries through to the proteins. All of the bioreps are normalized to the first biorep of the first condition, so it is assumed that most of the proteome is not changing between conditions or bioreps.