METHODS FOR GENERATING, SEARCHING AND STATISTICALLY VALIDATING A PEPTIDE FRAGMENT ION LIBRARY

Methods for generating, searching, and statistical validation of tandem mass spectra generated on a unique mass spectrometer system are disclosed. Library generation methods apply quality control measures to generate a high-quality local mass spectral library, such as of peptides, from matches to entries in general or public mass spectral libraries. Local library searching methods apply a multiple regression model to identify and score new experimental data against the generated library. An f-test can be computed to estimate the validity of a regression model. If the f-test passes, it indicates that at least one or more calculated coefficients are statistically significant. Each coefficient can then also be tested in terms of its respective statistical contribution to the model's validity, using a t-test. Since a spectrum is represented as a linear combination, if multiple coefficients are statistically significant, then multiplexed spectra are indicated.