Combinatorial libraries can be characterized in detail by high resolving power mass spectrometry. We here demonstrate this for synthetic decapeptide libraries using a state-of-the-art 15 T Fourier transform ion cyclotron resonance mass spectrometer. Using comparison between predicted and measured spectra, a number of metrics can be derived that shed light on the library composition and degeneracy of elemental compositions. These techniques can be used to rapidly quality control combinatorial synthesis products or follow combinatorial libraries in more detail, for instance during binding studies or chemical reactions. The methods are in principle equally applicable to the analysis of other types of combinatorial libraries.