Exploring the use of MS/MS spectral libraries to improve protein identification and characterization

The use of tandem mass spectrometry (MS/MS) is a well established method to identify and characterize proteins from complex samples. Various tools are designed to map MS/MS spectra to peptides and proteins. The most commonly used software are Sequest, Mascot, and Phenyx, often referred to as sequence search tools, as they employ a spectrum identification algorithm where the experimental spectra are compared to theoretical spectra generated in silico from a protein sequence database. In recent years, a different method for protein identification based on spectral library search has shown promising results. In this approach the sequence database is replaced by a collection of high quality MS/MS spectra confidently identified in previous analysis. This thesis is made up of four papers contributing to the development of an analysis workflow, combining the two identification strategies, to improve upon protein identification and characterization.