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

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dc.abstract.enElectron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists of several concurrent reactions triggered by the transfer of an electron from its anion source to sample cations. Transferring an electron causes peptide backbone cleavage while leaving labile post-translational modifications intact. The obtained fragmentation spectra provide valuable information for sequence and structure analyses. In this study, we propose a formal mathematical model of the ETD fragmentation process in the form of a system of stochastic differential equations describing its joint dynamics. Parameters of the model correspond to the rates of occurring reactions. Their estimates for various experimental settings give insight into the dynamics of the ETD process. We estimate the model parameters from the relative quantities of fragmentation products in a given mass spectrum by solving a nonlinear optimization problem. The cost function penalizes for the differences between the analytically derived average number of reaction products and their experimental counterparts. The presented method proves highly robust to noise in silico. Moreover, the model can explain a considerable amount of experimental results for a wide range of instrumentation settings. The implementation of the presented workflow, code-named ETDetective, is freely available under the two-clause BSD license.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorMiasojedow, Błażej
dc.contributor.authorGambin, Anna
dc.contributor.authorValkenborg, D.
dc.contributor.authorSobott, F.
dc.contributor.authorŁącki, Mateusz
dc.contributor.authorLermyte, F.
dc.contributor.authorCiach, M. A.
dc.date.accessioned2024-01-24T23:22:58Z
dc.date.available2024-01-24T23:22:58Z
dc.date.issued2018
dc.description.financeNie dotyczy
dc.description.number3
dc.description.volume25
dc.identifier.doi10.1089/CMB.2017.0156
dc.identifier.issn1066-5277
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/106414
dc.identifier.weblinkhttps://www.liebertpub.com/doi/10.1089/cmb.2017.0156
dc.languageeng
dc.pbn.affiliationcomputer and information sciences
dc.relation.ispartofJournal of Computational Biology
dc.relation.pages282-301
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.titleEstimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry
dc.typeJournalArticle
dspace.entity.typePublication