how to explain SNPs and proteomics data

[biocc]

Hi everyone,
We did comparative proteomics between a mutant and wide type strain. For understanding the reason of changes at the protein level, we re-sequenced the mutant strain. we detected some SNPs, but almost no SNP located CDS whose protein has changes in proteomics data. What I mean is the relation between SNPs and Proteomics data could not be found by direct analyses. Then what should I do?
please give me some suggestion. Thanks

[jujubix]

Are you considering the possibility of differences in transcript modification? (i.e. RNA editing) These could explain changes in the protein without any changes in the genome that you're seeing.