MaxQuant label-free quantification

[chenna...@gmail.com]

Hi,

When I use MaxQuant for the LFQ analysis. I found some proteins from my experimental sample have high intensities and several peptides. Their intensities are 0 in the control sample. I am very interested in those proteins. But their LFQ intensities are 0 in both samples.  I can not use imputation for the ratio calculation. I have used the "stabilize large LFQ ratio". Could someone help me understand it?

Best,

Nan