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Table 2 Scaling of the database size and functional transformation to yield calibrated E-values.

From: Calibrating E-values for MS2 database search methods

Method reported x db x1gr = xdb (1gr/db_size)α E = f(x1gr)
SEQUEST X-correlation xdb = e-(X-correlation) x1gr = xdb (1gr/db_size)-0.176 f(x1gr) = e10.59 x1gr4.11
InsPecT MQ_score xdb = e-(MQ_score) x1gr = xdb (1gr/db_size)-1 f(x1gr) = [e16.08 x1gr 1.4]1/2 if x1gr ≥ 0.148
     f(x1gr) = [e2.78 x1gr 0.48]1/2 if x1gr > 0.148
ProbID Posterior Prob. xdb = e-(Posterior Prob.) x1gr = xdb (1gr/db_size)-5 f(x1gr) = e13.82 x1gr 0.17
Mascot E-value xdb = E-value x1gr = xdb (1gr/db_size)0.301 f(x1gr) = x1gr/225
X!Tandem E-value xdb = E-value x1gr = xdb f(x1gr) = x1gr/10
OMSSA E-value xdb = E-value x1gr = xdb (1gr/db_size)-0.301 f(x1gr) = e-2.26 x1gr 0.57
RAId_Dbs E-value xdb = E-value x1gr = xdb E = f(x1gr) = x1gr
  1. Scaling of the database size and functional transformation to yield calibrated E-values. The calibration is done in two steps: first transform a database-size-dependent variable xdb (e.g. e-(X-correlation) for SEQUEST and E-value for X!Tandem) into a standard one, x1gr, which is calibrated for database size of 1 giga residues; second, a functional transformation f(x1gr) to yield the correct E-value given the equivalent variable x1gr. The symbol db_size, as suggested by its name, represents the size of the database used in a search. Note that the size scaling and the functional transformations may vary from laboratory to laboratory. However, once calibrated, it becomes sensible to compare the search results from different laboratories using different machines and different analysis software.