Natural or synthetic cyclic peptides often possess pronounced bioactivity. Their mass spectrometric characterization is difficult due to the predominant occurrence of non-proteinogenic amino acid monomers and the complex fragmentation patterns observed. Even though several software tools for the annotation of cyclic peptide tandem mass spectra have been published, these tools are still unable to annotate a majority of the signals observed in experimentally obtained spectra. They are thus not suitable for extensive mass spectrometric characterization of these compounds.

This lack of an advanced and user-friendly software tool has motivated us to extend the fragmentation module of a freely available open-source software, mMass (http://www.mmass.org), to allow for cyclic peptide tandem mass spectra annotation and interpretation. The resulting software has been tested on several cyanobacterial and other naturally occurring peptides and has been found to be superior to all other tools currently available with regard to both usability and annotation extensiveness. Thus it is highly useful for accelerating the structure confirmation and elucidation of cyclic as well as linear peptides and depsipeptides.

• annotation
• in-silico fragmentation
• mass spectrometry
• cryptophycin
• open source
• depsipeptides
• software
• microcystin
• cyclic peptides
• tandem mass spectra

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