Mass spectrometry (MS) is one of the most important techniques for high-throughput analysis in proteomics research. Due to the large number of different proteins and their post-translationally modified variants, the amount of data generated by a single wet-lab MS experiment can easily exceed several gigabytes. Hence, the time necessary to analyze and interpret the measured data is often significantly larger than the time spent on sample preparation and the wet-lab experiment itself. Since the automated analysis of this data is hampered by noise and baseline artifacts, more sophisticated computational techniques are required to handle the recorded mass spectra. Obviously, there is a clear tradeoff between performance and quality of the analysis, which is currently one of the most challenging problems in computational proteomics.