I have 2D spots which were stained with mass compatible silver staining method. I got reasonable MS peaks following in gel digestion, but unfortunately protein scores are lower than significancy level predicted by Mascot tool. How can I manage to increase protein score? And also, all peaks represent the same spot do not give the same result. Do the all peaks have to give same result in Mascot search? (For instance, DnaJ is the first score in a one peak, but 7th in other). It would be very much appreciated if you could help me.