Normalizing protein intensities

[acesnik]

iBAQ protein quantification excludes missed cleavages and normalizes intensities by the number of theoretical peptides, which correlates with length.

It looks like proteins with many quantified missed cleavages peptides and longer proteins are biased to higher protein intensities in MetaMorpheus, so performing similar normalizations are something to consider.

[acesnik]

I calculated the iBAQ intensities based on the MM quantified peptides.