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Improving protein sequencing methods

Date of news: 30 November 2018

To study the biological function of a protein, knowing the sequence of the hundreds of amino acids it contains is essential. Mass spectrometry is widely used to identify this sequence. The protein of interest is first dissociated into small peptides. Thousands of peptides can be introduced to the mass spectrometer. Powerful algorithms can match the data from possible peptide sequences in databases.

One way to dissociate a protein is electron-induced. This is a common method, but not fully understood. How does a protein dissociate exactly and which structures are then formed? FELIX researchers Lisanne Kempkes, Jonathan Martens, Giel Berden and Jos Oomens  investigated a comprehensive set of specific protein fragments from which two possible structures could be formed. By using infrared ion spectroscopy combined with quantum-chemical calculations they revealed the molecular structures of product ions and proved that of the two structures, one can likely be disregarded in general. The fundamental knowledge on chemical reactions they gained helps to improve the protein sequencing methods.

Spectroscopic Characterization

Experimental spectra of c3 and c4 ETD fragment ions (black) compared with the computed spectra for the amide structure (top, blue) and for the enol-imine isomer (red, below).


Lisanne J. M. Kempkes, Jonathan Martens, Giel Berden and Jos Oomens, "Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers", The Journal of Physical Chemistry Letters 9 (2018) 6404-6411.

More information: Giel Berden