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Structural characterization of MS/MS product ions from protonated peptides

The fragmentation behavior of a molecule is entirely governed by its molecular structure. Therefore, fragmentation mass spectrometry (MS/MS) is a common method for small-molecule identification. Identification of molecules may then be conducted by comparing their MS/MS fragmentation patterns with those listed in MS/MS libraries. However, data is available only for a limited subset of molecules, as reference standards are often not readily available.

Unreliable predictions

Therefore, various computational tools have been developed to predict fragmentation patterns, adopting rather empirical “fragmentation rules”. However, molecular dissociation is a complicated process dependent on the shape of the potential energy surface at high internal energies, which are not known and which are generally difficult to compute using quantum chemistry. As a consequence, the predicted MS/MS spectra are often unreliable.

Accurate determination

Infrared ion spectroscopy in combination with quantum-chemical calculations can provide detailed molecular structure information of any gas-phase ion isolated in a mass spectrometer, including MS/MS fragment ions. Our extensive work on peptide dissociation has for instance shown that we can accurately determine fragment ion structures. We noted that our spectroscopically identified structures often deviate entirely from predicted structures in in-silico MS/MS databases. This is also the case for small molecule components as suggested in our recent publication on the fragmentation of L-lysine to pipecolic acid. We think that annotated structures in in-silico databases are bogus in general because (some of) the underlying assumptions on fragmentation pathways are unphysical. We test our hypothesis on a selection of small molecules for which we will critically evaluate the structures of the MS/MS fragment ions.

Publications


Water Loss from Protonated XxxSer and XxxThr Dipeptides Gives Oxazoline—Not Oxazolone—Product Ions
Jos Oomens, Lisanne J. M. Kempkes, Thijs P. J. Geurts, Luuk van Dijk, Jonathan Martens, Giel Berden, and P. B. Armentrout
J. Am. Soc. Mass Spectrom. 2020, 31, 10, 2111–2123
https://doi.org/10.1021/jasms.0c00239

Influence of a Hydroxyl Group on the Deamidation and Dehydration Reactions of Protonated Asparagine-Serine Investigated by Combined Spectroscopic, Guided Ion Beam, and Theoretical Approaches
Georgia C. Boles, Lisanne J. M. Kempkes, Jonathan Martens, Giel Berden, Jos Oomens, and P. B. Armentrout
J. Am. Soc. Mass Spectrom. 2021, 32, 3, 786–805
https://doi.org/10.1021/jasms.0c00468


Ion spectroscopy and guided ion beam studies of protonated asparaginyl-threonine decomposition: Influence of a hydroxyl containing C-Terminal residue on deamidation processes
Georgia C. Boles, Lisanne J.M.Kempkes, Jonathan Martens, Giel Berden, Jos Oomens, P.B.Armentrout
International Journal of Mass Spectrometry 2019, 442, 64-82
https://doi.org/10.1016/j.ijms.2019.05.010

Investigation of the position of the radical in z3-ions resulting from electron transfer dissociation using infrared ion spectroscopyLisanne J. M. Kempkes, Jonathan Martens, Giel Berden, Kas J. Houthuijs and Jos Oomens
Faraday Discuss., 2019, 217, 434-452
https://doi.org/10.1039/C8FD00202A

Deamidation of Protonated Asparagine–Valine Investigated by a Combined Spectroscopic, Guided Ion Beam, and Theoretical Study
L.J.M. Kempkes, G.C. Boles, J. Martens, G. Berden, P.B. Armentrout, and J. Oomens
J. Phys. Chem. A 2018, 122, 9, 2424–2436
https://doi.org/10.1021/acs.jpca.7b12348

Dehydration reactions of protonated dipeptides containing asparagine or glutamine investigated by infrared ion spectroscopy
L.J.M. Kempkes, J. Martens, G. Berden, and J. Oomens
International Journal of Mass Spectrometry 208, 429, 90-100
https://doi.org/10.1016/j.ijms.2017.06.004

Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers
Lisanne J.M. Kempkes, Jonathan Martens, Giel Berden, and Jos Oomens
J. Phys. Chem. Lett. 2018, 9, 22, 6404–6411
https://doi.org/10.1021/acs.jpclett.8b02850

w‐Type ions formed by electron transfer dissociation of Cys-containing peptides investigated by infrared ion spectroscopy
L.J.M. Kempkes, J. Martens, G. Berden, and J. Oomens
Journal of Mass Spectrometry 2018, 53, 1207-1213
https://doi.org/10.1002/jms.4298