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

J 2022

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 et. al.

Základní údaje

Originální název

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

Autoři

YASSAGHI, Ghazaleh, Zdenek KUKACKA, Jan FIALA, Daniel KAVAN, Petr HALADA, Michael VOLNY a Petr NOVAK

Vydání

Analytical chemistry, WASHINGTON, AMER CHEMICAL SOC, 2022, 0003-2700

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10406 Analytical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 7.400

Kód RIV

RIV/00216224:14740/22:00128782

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/acs.analchem.1c05476

UT WoS

000829261100001

Klíčová slova anglicky

Dissociation; Electron transitions; Ions; Mass spectrometry; Oxidation; Photochemical reactions; Structural dynamics

Štítky

ne MU, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 2. 2023 19:45, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

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.

Návaznosti

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

YASSAGHI, Ghazaleh, Zdenek KUKACKA, Jan FIALA, Daniel KAVAN, Petr HALADA, Michael VOLNY a 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, roč. 94, č. 28, s. 9993-10002. ISSN 0003-2700. Dostupné z: https://dx.doi.org/10.1021/acs.analchem.1c05476.

@article{2262573,
   author = {Yassaghi, Ghazaleh and Kukacka, Zdenek and Fiala, Jan and Kavan, Daniel and Halada, Petr and Volny, Michael and Novak, Petr},
   article_location = {WASHINGTON},
   article_number = {28},
   doi = {http://dx.doi.org/10.1021/acs.analchem.1c05476},
   keywords = {Dissociation; Electron transitions; Ions; Mass spectrometry; Oxidation; Photochemical reactions; Structural dynamics},
   language = {eng},
   issn = {0003-2700},
   journal = {Analytical chemistry},
   title = {Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation,Electron-Transfer Dissociation, and Electron-Capture Dissociation},
   url = {https://pubs.acs.org/doi/10.1021/acs.analchem.1c05476},
   volume = {94},
   year = {2022}
}

TY  - JOUR
ID  - 2262573
AU  - Yassaghi, Ghazaleh - Kukacka, Zdenek - Fiala, Jan - Kavan, Daniel - Halada, Petr - Volny, Michael - Novak, Petr
PY  - 2022
TI  - Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation,Electron-Transfer Dissociation, and Electron-Capture Dissociation
JF  - Analytical chemistry
VL  - 94
IS  - 28
SP  - 9993-10002
EP  - 9993-10002
PB  - AMER CHEMICAL SOC
SN  - 00032700
KW  - Dissociation
KW  - Electron transitions
KW  - Ions
KW  - Mass spectrometry
KW  - Oxidation
KW  - Photochemical reactions
KW  - Structural dynamics
UR  - https://pubs.acs.org/doi/10.1021/acs.analchem.1c05476
N2  - 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.
ER  -

YASSAGHI, Ghazaleh, Zdenek KUKACKA, Jan FIALA, Daniel KAVAN, Petr HALADA, Michael VOLNY a Petr NOVAK. Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation,Electron-Transfer Dissociation, and Electron-Capture Dissociation. \textit{Analytical chemistry}. WASHINGTON: AMER CHEMICAL SOC, 2022, roč.~94, č.~28, s.~9993-10002. ISSN~0003-2700. Dostupné z: https://dx.doi.org/10.1021/acs.analchem.1c05476.

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