Results are usually returned with some sort of probability estimate (depending on the software we use) and usually a false discovery rate (FDR). You can have a look at our Scaffold Quick Start Guide 4.0 for some more info. To make a long story short, we cannot guarantee the results you get are 100% correct. No one really can with this type of data unfortunately. The best advice is to please call before you spend a lot of money making an antibody or designing expensive experiments if you are not really familiar with this type of data.
Here is an excellent paper that explains multiple testing correction, FDR’s, p-values and q-values