Partial sequencing of peptides using fragment mass spectra: algorithm and testing

A new algorithm is developed for partial sequencing of peptides using MS/MS spectra for peptide sequence tag search. To accelerate the algorithm, it is optimized by reducing the number of tested sequence hypotheses. To evaluate sequence hypotheses a Bayesian approach is employed, based upon the actual statistics of mass specral peaks. The algorithm has been tested using data from a tandem Q-TOF MS as well as from Bruker Esquire mass spectrometer based on the Pauli ion trap.