Conformational changes of ubiquitin during electrospray ionization as determined by in‐ESI source H/D exchange combined with high‐resolution MS and ECD fragmentation

Kostyukevich, Yury; Kononikhin, Alexey; Popov, Igor; Nikolaev, E. N.

doi:10.1002/jms.3409

Cited by 44 publications

(41 citation statements)

References 43 publications

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“…This result is unexpected because the low CS correspond to the folded gas‐phase conformers and high CS to the unfolded ones. But it is in agreement with the previously performed H/D exchange experiments . It was demonstrated many times that gas‐phase H/D exchange performed in the high vacuum part of the mass spectrometer produces a multi‐modal isotopic distribution suggesting the existence of different conformations with different H/D exchange rates .…”

Section: Resultssupporting

confidence: 91%

Supermetallization of peptides and proteins during electrospray ionization

et al. 2015

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The formation of metal-peptide complexes during electrospray ionization (ESI) is a widely known phenomenon and is often considered to be undesirable. Such effect considerably limits the use of ESI mass spectrometry for the investigation of biologically relevant metal-peptide compounds that are present in the solution and play critical roles in many bioprocesses such as progression of neurodegenerative diseases. In the article, it is demonstrated that under specific conditions such as high temperature of the desolvating capillary, an interesting effect, which can be called as 'supermetallization', occurs. Using a model peptide Αβ amyloid domain 1-16, it was observed that an increase in the temperature of the desolvating capillary results in multiple substitutions of hydrogen atoms by Zn atoms in this peptide. At high temperatures (T ~ 400 °C), up to 11 zinc atoms can be covalently bound to (1-16) Αβ. It was observed that supermetallization of (1-16) Αβ depends on the solvent composition and pH. Supermetallization was also demonstrated for proteins, such as ubiquitin and cytochrome C. That proves that the supermetallization is a general phenomenon for peptides and proteins. For the structural investigation of supermetallized complexes, electron-capture dissociation (ECD) fragmentation was applied. The effect of hydrogen rearranging during ECD was observed. In addition, quantum chemical calculations were used to estimate the possible structures of different supermetallized complexes. These results allow a more deep understanding of the limitations of the use of ESI mass spectrometry for the investigation of biologically relevant metal-peptide complexes. Copyright © 2015 John Wiley & Sons, Ltd.

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Section: Resultssupporting

confidence: 91%

Supermetallization of peptides and proteins during electrospray ionization

et al. 2015

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“…The Clemmer group reported the retention of native compact conformers for the same dominant charge states observed in our experiment [38, 39]. In the current configuration and solution conditions, the 3 + charge state was observed and is lower than reported by our group and others, suggesting the REIS is a “cold” source [6, 40, 41]. …”

Section: Resultssupporting

confidence: 81%

Development and Evaluation of a Reverse-Entry Ion Source Orbitrap Mass Spectrometer

Poltash

McCabe

Patrick

et al. 2018

J. Am. Soc. Mass Spectrom.

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As a step towards development of a high-resolution ion mobility mass spectrometer using the orbitrap mass analyzer platform, we describe herein a novel reverse-entry ion source (REIS) coupled to the higher-energy C-trap dissociation (HCD) cell of an orbitrap mass spectrometer with extended mass range. Development of the REIS is a first step in the development of a drift tube ion mobility-orbitrap MS. The REIS approach retains the functionality of the commercial instrument ion source which permits the uninterrupted use of the instrument during development as well as performance comparisons between the two ion sources. Ubiquitin (8.5 kDa) and lipid binding to the ammonia transport channel (AmtB, 126 kDa) protein complex were used as model soluble and membrane proteins, respectively, to evaluate the performance of the REIS instrument. Mass resolution obtained with the REIS is comparable to that obtained using the commercial ion source. The charge state distributions for ubiquitin and AmtB obtained on the REIS are in agreement with previous studies which suggests that the REIS-orbitrap EMR retains native structure in the gas phase. Graphical Abstract ᅟ.

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“…In general, ions trapped for varied lengths of time are exposed to labelling reagents. Alternatively, the source region of the mass spectrometer can be modified to introduce labelling reagents [69][70][71][72]. The pressure of the deuterated reagent depends on the trapping device: in the 10 À8 Torr range for ion cyclotron resonance (ICR) cells [73][74][75] and higher for multipole ion reservoirs [20,76,77].…”

Section: Gas-phase Hdx-msmentioning

confidence: 99%

Mass spectrometric methods to analyze the structural organization of macromolecular complexes

Rajabi

Ashcroft

Radford

2015

Methods

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With the development of soft ionization techniques such as electrospray ionization (ESI), mass spectrometry (MS) has found widespread application in structural biology. The ability to transfer large biomolecular complexes intact into the gas-phase, combined with the low sample consumption and high sensitivity of MS, has made ESI-MS a method of choice for the characterization of macromolecules. This paper describes the application of MS to study large non-covalent complexes. We categorize the available techniques in two groups. First, solution-based techniques in which the biomolecules are labeled in solution and subsequently characterized by MS. Three MS-based techniques are discussed, namely hydroxyl radical footprinting, cross-linking and hydrogen/deuterium exchange (HDX) MS. In the second group, MS-based techniques to probe intact biomolecules in the gas-phase, e.g. side-chain microsolvation, HDX and ion mobility spectrometry are discussed. Together, the approaches place MS as a powerful methodology for an ever growing plethora of structural applications.

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Conformational changes of ubiquitin during electrospray ionization as determined by in‐ESI source H/D exchange combined with high‐resolution MS and ECD fragmentation

Cited by 44 publications

References 43 publications

Supermetallization of peptides and proteins during electrospray ionization

Supermetallization of peptides and proteins during electrospray ionization

Development and Evaluation of a Reverse-Entry Ion Source Orbitrap Mass Spectrometer

Mass spectrometric methods to analyze the structural organization of macromolecular complexes

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