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Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry

  • Michał Aleksander CiachEmail author
  • Mateusz Krzysztof ŁąckiEmail author
  • Błażej Miasojedow
  • Frederik Lermyte
  • Dirk Valkenborg
  • Frank Sobott
  • Anna Gambin
Conference paper
  • 1.6k Downloads
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10330)

Abstract

Electron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists of several competing reactions triggered by the transfer of an electron from its anion source to the sample cations. One can retrieve relative quantities of the products from mass spectra.

We present a method to analyze these results from the perspective of the reaction kinetics. A formal mathematical model of the ETD process is introduced and parametrized by intensities of the occurring reactions. Also, we introduce a method to estimate the reaction intensities by solving a nonlinear optimization problem. The presented method proves highly robust to noise on in silico generated data. Moreover, the presented model can explain a considerable amount of experimental results obtained under various experimental settings.

Keywords

Molecular Species Basic Amino Acid Electron Transfer Dissociation Backbone Cleavage Reaction Graph 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

This work was partially supported by the National Science Centre grants number 2013/09/B/ST6/01575, 2014/12/W/ST5/00592 and 2015/17/N/ST6/03565, the SBO grant InSPECtor (120025) of the Flemish agency for Innovation by Science and Technology (IWT). The authors thank the Research Foundation – Flanders (FWO) for funding a Ph.D. fellowship (F.L.). The Synapt G2 mass spectrometer is funded by a grant from the Hercules Foundation – Flanders.

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Michał Aleksander Ciach
    • 1
    Email author
  • Mateusz Krzysztof Łącki
    • 1
    Email author
  • Błażej Miasojedow
    • 1
  • Frederik Lermyte
    • 2
    • 3
  • Dirk Valkenborg
    • 3
    • 4
  • Frank Sobott
    • 2
  • Anna Gambin
    • 1
  1. 1.Faculty of Mathematics, Informatics and MechanicsUniversity of WarsawWarsawPoland
  2. 2.Biomolecular and Analytical Mass Spectrometry Group, Department of ChemistryUniversity of AntwerpAntwerpBelgium
  3. 3.Centre for ProteomicsUniversity of AntwerpAntwerpBelgium
  4. 4.Interuniversity Institute for Biostatistics and Statistical BioinformaticsHasselt UniversityHasseltBelgium

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