Is there a way to perform GO enrichment including the number of times the same protein was found with different peptides?

Question

[nitrushina]

I am performing GO enrichment analysis based on data from mass-spectrometry. Sometimes I have more than one peptide with interesting modification for one protein. So when I see a change in several peptides I want this information to also be included in GO term analysis. Now I have a list of genes for making GO enrichment graphs, however all programs I have used so far just remove the duplicates of the same genes. Can one include information on how many same genes are found into such analysis?