Proteins are involved in essentially any cellular process and constitute key players in the regulation of biological systems. The scope of this book focusses on computational methods that support analytical approaches for the quantification of proteins. Liquid chromatography coupled to mass spectrometry (LC-MS) is a popular technique for the characterization of protein mixtures. This book addresses the challenges of LC-MS based approaches and describes a novel computational framework for the in-depth analysis of large scale mass spectrometry data sets. In particular, the software SuperHirn for the detection and quantification of protein signals is introduced. In addition, the concept of the MasterMap as a comprehensive repository for the storage of extracted and processed protein signals is presented. The functionalities of SuperHirn and the MasterMap are highlighted by the quantification and classification of protein abundance changes in complex biological samples. The convenience of the introduced computational methodology is further discussed in different applications addressing emerging topics in protein-centered biology.
