The P Score is a statistical model of MS/MS matching based on the Poisson Distribution.

• If an event is expected to occur λ times, then the probability of it occurring k times is given by the Poisson distribution:

• If f is the total number of observed fragments, and n is the number of matching fragments, we may estimate the probability of a random protein match given f and n:

where x is the mean probability that a mass of an observed fragment ion will randomly match one from a generic protein.

• Given the probability of a random protein match with a particular n, f, and Ma, we can now estimate the probability of getting a match at least as good as we have by random chance:

where p is the p-value assuming our Poisson model – what we call the P Score.