1. A method for defining a misidentification probability for an experimental protein divisible into experimental peptides, the method comprising: receiving data representing a set of matches of experimental peptides to reference peptides that can be derived from a protein in a database of proteins; calculating a probability of observing by chance, in a search of the database of proteins, a set of matches equivalent to or better than the represented set of matches; and defining the misidentification probability using the probability of observing by chance a set of matches equivalent to or better than the represented set of matches.