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

Diplôme Thèse Exploring the use of MS/MS spectral libraries to improve protein identification and characterization eng 2011-05-06 author Ahrne Erik 639104 director Appel Ron David 22305 director Lisacek Frédérique 0000-0002-0948-4537 639315 10.13097/archive-ouverte/unige:16383 urn:nbn:ch:unige-163835 Sc. 4311 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. Dewey 025.063 13 Centre universitaire d'informatique 0D3 32 Département d'informatique 18 false 405b9ec3-ed88-49e8-9c17-4f861cf66d82 Swiss Institute of Bioinformatics (SIB) ffbff934-36e1-471b-87f3-6f869c9e14a1 Thesis Public E_Ahrne_Thesis.pdf 6741348 application/pdf openAccess Centres et instituts / Centre universitaire d'informatique Faculté des sciences / Département d'informatique

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Ahrne, Erik