Interpretation of ESI(+)-MS-MS spectra—Towards the identification of “unknowns”

We report a systematic empirical investigation of ESI(+)-MS-MS dissociation pathways of over 1000 spectra of small organic compounds, containing more than 30 chemical functional groups. The dissociation processes of the protonated molecular ions were explored and interpretated. We derived typical basic fragmentation channels for individual functional groups and established a unified set of fragmentation rules. Multiple bond cleavages of molecules containing single and multiple functional groups were explored as well and the corresponding fragmentation rules were derived. Applying these rules enabled to match between proposed chemical structures and an ESI(+)-MS-MS spectrum of an “unknown”. Comparison to EI fragmentation routes was also carried out. Despite the general dissimilarity between ESI(+)-MS-MS and EI-MS spectra, we exploit the minor similarities between the spectra, and utilizing NIST-EI database and search option, can be successfully reduced the number of proposed structures. The two step methodology developed here is demonstrated and evaluated in the identification of various “unknowns”.

Figure optionsDownload high-quality image (75 K)Download as PowerPoint slideResearch highlights▶ A new set of fragmentation rules for more than 30 functional groups, based on interpretation of over 1000 ESI library spectra was established. Multiple bond cleavages of molecules containing single and multiple functional groups were also explored. ▶ The rules suggest a limited number of realistic fragmentation pathways of protonated chemical structures originated by ESI-MS-MS. ▶ EI search option and large database are used as a tool for reducing the list of possible structures for an ESI-MS-MS spectrum. ▶ This work outcome may be implemented in automated search and interpretation algorithms as part of “unknown” identification processes of small molecules.