A P-Score is the probability of obtaining at least as good a match between the observed fragment list and a sequence as by chance. It is a measure of confidence in the validity of a match. A low P-Score means that the probability of obtaining at least this many fragments matching a sequence is low. Thus, an association caused by random chance is unlikely.

The application calculates a P-Score as follows:

where:

  • n is the number of matching fragments.
  • x is the probability of an observed fragment ion matching a random theoretical fragment ion by chance.
  • f is the total number of fragment ions observed.

Matching more fragment ions leads to a lower, more confident P-Score. Alternatively, increasing the numbers of total detected fragment ions without a corresponding increase in matched fragment ions negatively affects the confidence of the result. To see the original score derivation, refer to:

https://www.nature.com/articles/nbt1001-9521)