Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation,Electron-Transfer Dissociation, and Electron-Capture Dissociation

YASSAGHI, Ghazaleh, Zdenek KUKACKA, Jan FIALA, Daniel KAVAN, Petr HALADA, Michael VOLNY and Petr NOVAK. Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation,Electron-Transfer Dissociation, and Electron-Capture Dissociation. Analytical chemistry. WASHINGTON: AMER CHEMICAL SOC, 2022, vol. 94, No 28, p. 9993-10002. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.1c05476.

Basic information

• Original name: Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation,Electron-Transfer Dissociation, and Electron-Capture Dissociation
• Authors: YASSAGHI, Ghazaleh, Zdenek KUKACKA, Jan FIALA, Daniel KAVAN, Petr HALADA, Michael VOLNY and Petr NOVAK.
• Edition: Analytical chemistry, WASHINGTON, AMER CHEMICAL SOC, 2022, 0003-2700.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10406 Analytical chemistry
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 7.400
• RIV identification code: RIV/00216224:14740/22:00128782
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1021/acs.analchem.1c05476
• UT WoS: 000829261100001
• Keywords in English: Dissociation; Electron transitions; Ions; Mass spectrometry; Oxidation; Photochemical reactions; Structural dynamics
• Tags: ne MU, rivok
• Tags: International impact, Reviewed

Abstract

Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical reactions. The position of oxidative modification reflects solvent accessibility and site reactivity and thus provides information about protein conforma-tion, structural dynamics, and interactions. Bottom-up mass spectrometry is an established standard method to analyze FPOP samples. In the bottom-up approach, all forms of the protein are digested together by a protease of choice, which results in a mixture of peptides from various subpopulations of proteins with varying degrees of photochemical oxidation. Here, we investigate the possibility to analyze a specifically selected population of only singly oxidized proteins. This requires utilization of more specific top-down mass spectrometry approaches. The key element of any top-down experiment is the selection of a suitable method of ion isolation, excitation, and fragmentation. Here, we employ and compare collision-induced dissociation, electron-transfer dissociation, and electron-capture dissociation combined with multi-continuous accumulation of selected ions. A singly oxidized subpopulation of FPOP-labeled ubiquitin was used to optimize the method. The top-down approach in FPOP is limited to smaller proteins, but its usefulness was demonstrated by using it to visualize structural changes induced by co-factor removal from the holo/apo myoglobin system. The top-down data were compared with the literature and with the bottom-up data set obtained on the same samples. The top-down results were found to be in good agreement, which indicates that monitoring a singly oxidized FPOP ion population by the top-down approach is a functional workflow for oxidative protein footprinting.

Links

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