Proteomics is the systematic study of all proteins. State-of-the-art methods based on mass spectrometry can detect, identify and quantify thousands of proteins simultaneously in one experiment. A critical component of this technology is the computational methods to deduce peptide or protein sequences from fragmentation patterns of these molecules collected in the mass spectrometer. This project focuses on improving the existing data analysis methods in various aspects such as speed, sensitivity, range of applicability and ease of use.