Any one familiar with IP-MS data analysis?

Question

[shuaizh117]

I have a dataset from an IP-MS experiment. In the excel, I have the spectral counts for "pre clear" (as background) in addition to the spectral counts for prey proteins. I assume to perform DE analysis, I need to substract "pre-clear" counts first, however, some of the spectral counts became negative or zero after substracting "pre-clear" counts. Because I plan to use limma to perform DE analysis on these values, so I wonder how should I deal with negative values and zero? Is it reasonable if I just assign them with an extreme small value as 1? Thanks!