How to analyse RNA-based protein pulldown mass spectrometry data

Question

[PK]

Hi to all,

I did the RNA-based protein pulldown IP's for the mass spectrometry (without TMT labelling). I got the peptide counts and lot of them were zero. So i did log2(x+1) to all the data. since i have huge number of zeros, it is influencing my data. My volcano plot from limma kind of flattened. There is a one major point is, i have zero peptide count in control but some values in expriment (e.g count is 5). I have to consider such values, because it is RNA based protein pulldown. So i did not expect huge number of peptide counts. I have IBAQ values and RAW peptide count as well. What will be the better way to analyse such data. can you please help me with this.