A Combinatorial Approach to Protein Mixture - Identification based on Mass Spectrometry Data

Abstract

Protein mixture identification by Mass Spectrometry (MS) data using massmapping experiments has become a powerful method in identification, and in some cases quantification, of proteins in samples taken from tissues. The mainstream approaches for database search method usually impose an upper bound of 2 or 3 on the number of proteins in a sample mixture. In this thesis the problem in its most general from is reformulated as a hitting set problem over (finding transversals of) a hypergraph. The limitations and extent of applicability of this approach, considering different error sources in MS data are addressed.