Hi all,

I am relatively new to the proteomics. I am analysing my proteomics data which is the direct output of maxquant where i have iBAQ and LFQ values. i thought LFQ values are the better representation of iBAQ to get rid of outliers and others. But after i spent more time on data i found something because i have three replicates for each experiment. i have significant amount of values in iBAQ (for my protein of interest) but LFQ has nothing (two replicates were zero one replicate has some values). Can you please suggest me which one to consider and what is the real difference between iBAQ and LFQ values and they are calculated (some reference)

Thanks in advance