Mass spectrometry versus western blotting for validation
It is a common practice to prove a result using an orthogonal technique. Like RNAseq followed by qRT-PCR etc.

Western blotting is not a robust technique and cross comparisons are difficult because of difference in the avidities/affinities of different antibodies. So comparisons can be made only with one protein-control pair in different conditions. 

LC-MS is more sensitive and less biased(IMO). So the general trick is- don't do westerns for all proteins just report the ones that behave well (say that you "chose" these because they are important). I know this is a wrong practice and I should not be advocating it. For your own scientific validation try it with another MS technique; if you used ESI-Quadrupole/ion-Trap etc then try with MALDI-TOF or iTRAQ. Some luddites will continue to cling to westerns.

I think it is better to not test the proteins that have low peptide counts. See what is known as MA plot. This is frequently used for microarrays. Here M denotes fold change and A denotes total expression in both samples. Don't pick proteins that are low in expression in both samples; they might not be meaningful. For example if you have 2 molecules of X and 100 molecules of Y in control condition and 5 molecules of X and 200 molecules of Y in test; then the fold change in X would seem important; however this change may not be relevant and can be a result of stochastic fluctuation/measurement error. If you have many samples you can see if something is stochastic or not but the limitation is the number of samples. 

Note: I am not saying that 2→5 molecule increment should be meaningless. But to know if they have a meaning or not you would require more complex models; better avoid them at this moment.