A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins.

ABSTRACT: Identifying peptides from mass spectrometric fragmentation data (MS/MS spectra) using search strategies that map protein sequences to spectra is computationally expensive. An alternative strategy uses direct spectrum-to-spectrum matching against a reference library of previously observed MS/MS that has the advantage of evaluating matches using fragment ion intensities and other ion types than the simple set normally used. However, this approach is limited by the small sizes of the available peptide MS/MS libraries and the inability to evaluate the rate of false assignments. In this study, we observed good performance of simulated spectra generated by the kinetic model implemented in MassAnalyzer (Zhang, Z. (2004) Prediction of low-energy collision-induced dissociation spectra of peptides.

SUBMITTER: Yen CY 

PROVIDER: S-EPMC2667364 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature