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 (25%), 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.

(I asked the same question in Biostars but i did not get any answer so i posted here)

I am not at all famliar with RNA-based protein pulldown mass spectrometry, so I can't tell you how to analyse it. My first suggestion would be to try analysing it like RNA-seq, e.g., with edgeR::voomLmFit or edgeR::glmQLFit.