MaxQuant output quantifies the protein intensity in two ways :
Intensity (called LFQ intensity in a label-free experiment) : The combined intensity of the peptides of the protein.
iBAQ : A score attempting to make the intensity value comparable across different proteins. It is obtained by dividing the sum of protein intensities by the number of theoretically observable tryptic peptides (between 6 and 30 amino acids ).
It is said that usually it is better to just compare the Intensity score to identify differentially abundant proteins.
My question (which is for the sake of understanding) - why is it actually better? I understand from the definition of the iBAQ that the only difference between it and the LFQ is a division by a constant (same constant for all samples). So what makes it less preferable than LFQ for differential abundance calculation?
