Fine Structure in Isotopic Peak Distributions Measured Using a Dynamically Harmonized Fourier Transform Ion Cyclotron Resonance Cell at 7 T

Nikolaev, E. N.; Jertz, R.; Grigoryev, Anton; Baykut, Gökhan

doi:10.1021/ac202804f

Cited by 64 publications

(46 citation statements)

References 5 publications

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“…As we used a dynamically harmonized ICR cell [9,10] in the current work, the correction DC voltages are applied to the four inverse leaf electrode pairs (Supplementary Figure S1), all of which normally carry a common DC bias voltage. Therefore, the rf/ DC coupling network of the dynamically harmonized ICR cell [9,10] has been modified. A separate DC voltage is applied to each inverse leaf-shaped mantle electrode pair in each 90°d etection and excitation section.…”

Section: How To Correct the Offset Radial Electric Fieldmentioning

confidence: 99%

“…With the introduction of advanced ionization techniques like electrospray ionization (ESI) and related atmospheric pressure ionization techniques, as well as matrix assisted laser desorption ionization (MALDI), a substantial worldwide increase in FT-ICR MS applications followed not only in basic chemical research but also in life science biomolecular studies, as well as for the analysis of complex mixtures like petroleum or other complex natural products [4][5][6][7]. Recent instrumental developments in Fourier transform ion cyclotron resonance mass spectrometry [3,[8][9][10][11] reconfirm the role of FT-ICR as the mass spectrometric technique providing the highest mass resolving power even if moderate field strengths like 7 Tesla are used.…”

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confidence: 99%

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Tracking the Magnetron Motion in FT-ICR Mass Spectrometry

Jertz

Friеdrich

Kriete

et al. 2015

J. Am. Soc. Mass Spectrom.

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Abstract. In Fourier transform ion cyclotron resonance spectrometry (FT-ICR MS) the ion magnetron motion is not usually directly measured, yet its contribution to the performance of the FT-ICR cell is important. Its presence is manifested primarily by the appearance of even-numbered harmonics in the spectra. In this work, the relationship between the ion magnetron motion in the ICR cell and the intensities of the second harmonic signal and its sideband peak in the FT-ICR spectrum is studied. Ion motion simulations show that during a cyclotron motion excitation of ions which are offset to the cell axis, a position-dependent radial drift of the cyclotron center takes place. This radial drift can be directed outwards if the ion is initially offset towards one of the detection electrodes, or it can be directed inwards if the ion is initially offset towards one of the excitation electrodes. Consequently, a magnetron orbit diameter can increase or decrease during a resonant cyclotron excitation. A method has been developed to study this behavior of the magnetron motion by acquiring a series of FT-ICR spectra using varied post-capture delay (PCD) time intervals. PCD is the delay time after the capture of the ions in the cell before the cyclotron excitation of the ion is started. Plotting the relative intensity of the second harmonic sideband peak versus the PCD in each mass spectrum leads to an oscillating BPCD curve". The position and height of minima and maxima of this curve can be used to interpret the size and the position of the magnetron orbit. Ion motion simulations show that an off-axis magnetron orbit generates even-numbered harmonic peaks with sidebands at a distance of one magnetron frequency and multiples of it. This magnetron offset is due to a radial offset of the electric field axis versus the geometric cell axis. In this work, we also show how this offset of the radial electric field center can be corrected by applying appropriate DC correction voltages to the mantle electrodes of the ICR cell while observing the signals of the second harmonic peak group. The field correction leads to a definite performance increase in terms of resolving power and mass accuracy, and the mass spectrum contains intensity-minimized even-numbered harmonics. This is very important in the case of high performance cells, particularly the dynamically harmonized cell, since the magnetron motion can severely impair the averaging effect for dynamic harmonization and can therefore reduce the resolving power.

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Section: How To Correct the Offset Radial Electric Fieldmentioning

confidence: 99%

mentioning

confidence: 99%

Tracking the Magnetron Motion in FT-ICR Mass Spectrometry

Jertz

Friеdrich

Kriete

et al. 2015

J. Am. Soc. Mass Spectrom.

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“…Physical effects arising in FT-MS may also influence the measurement of isotopic abundances by an Orbitrap. These can include space charging and peak coalescence phenomena (40,41). Such effects are usually discussed in the context of mass accuracy, but they may also exert an influence on observed peak intensities when clouds of ions have near-equivalent m/z values.…”

Section: Isotopic Fidelity In Hdx-msmentioning

confidence: 99%

Platform Dependencies in Bottom-up Hydrogen/Deuterium Exchange Mass Spectrometry

Burns

Rey

Baker³

et al. 2013

Molecular & Cellular Proteomics

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Hydrogen-deuterium exchange mass spectrometry is an important method for protein structure-function analysis. The bottom-up approach uses protein digestion to localize deuteration to higher resolution, and the essential measurement involves centroid mass determinations on a very large set of peptides. In the course of evaluating systems for various projects, we established two (HDX-MS) platforms that consisted of a FT-MS and a highresolution QTOF mass spectrometer, each with matched front-end fluidic systems. Digests of proteins spanning a 20 -110 kDa range were deuterated to equilibrium, and figures-of-merit for a typical bottom-up (HDX-MS) experiment were compared for each platform. The Orbitrap Velos identified 64% more peptides than the 5600 QTOF, with a 42% overlap between the two systems, independent of protein size. Precision in deuterium measurements using the Orbitrap marginally exceeded that of the QTOF, depending on the Orbitrap resolution setting. However, the unique nature of FT-MS data generates situations where deuteration measurements can be inaccurate, because of destructive interference arising from mismatches in elemental mass defects. This is shown through the analysis of the peptides common to both platforms, where deuteration values can be as low as 35% of the expected values, depending on FT-MS resolution, peptide length and charge state. Hydrogen-deuterium exchange mass spectrometry (HDX-MS)1 provides a powerful means to study the link between protein structure and function (1). The method involves a chemical process in which labile hydrogens within a protein are exchanged with hydrogen from bulk water. When D 2 O is used in place of H 2 O, a mass shift results at every point of exchange, but it is the backbone amide hydrogens that offer exchange rates on a measurable timescale (2, 3). Measuring an amide hydrogen exchange rate can provide access to conformational dynamics, stability, and the interaction characteristics in that location of structure (4, 5). H/D exchange rates have be used to explore mechanisms of protein folding (6), determine the allosteric impact of post-translational modifications and ligand binding (7, 8), define truncation points for enhancing crystallization success (9), and they have also found a role in mapping interactions between proteins (10). Applications have stepped outside of primary research to include the characterization of protein drugs for stability and similarity testing (11-13). The capacity to provide such information has attracted increased attention from regulatory bodies and is generating a push for standardizing HDX methods. Mass spectrometers are very effective tools for measuring exchange rates, from whole proteins down to the individual amide levels. Classical methods of rate measurement have used NMR (3), but mass spectrometry offers all the advantages of speed, sensitivity and scale that have made the tool so useful in proteomics. Measurements at the peptide level provide an important intermediate resolution. As with bottom-up proteomics, r...

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“…Specifically, the transient lifetime has been substantially, about 10-to 100-fold, increased. The dynamically harmonized ICR cell, following the original idea of Boldin and Nikolaev [29], is particularly impressive, with demonstrated resolution of up to 40 million on a peptide (single peak) and a routinely achieved isotopic fine structure resolution on peptide ions even in moderate, 7 T, magnetic fields [31]. The main drawback of the harmonized cells is that they do not improve the throughput (or the acquisition rate) of FT-ICR MS.…”

Section: Introductionmentioning

confidence: 99%

Ion Trap with Narrow Aperture Detection Electrodes for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Nagornov

Kozhinov

Tsybin

et al. 2015

J. Am. Soc. Mass Spectrom.

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Abstract. The current paradigm in ion trap (cell) design for Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the ion detection with wide aperture detection electrodes. Specifically, excitation and detection electrodes are typically 90°wide and positioned radially at a similar distance from the ICR cell axis. Here, we demonstrate that ion detection with narrow aperture detection electrodes (NADEL) positioned radially inward of the cell's axis is feasible and advantageous for FT-ICR MS. We describe design details and performance characteristics of a 10 T FT-ICR MS equipped with a NADEL ICR cell having a pair of narrow aperture (flat) detection electrodes and a pair of standard 90°excitation electrodes. Despite a smaller surface area of the detection electrodes, the sensitivity of the NADEL ICR cell is not reduced attributable to improved excite field distribution, reduced capacitance of the detection electrodes, and their closer positioning to the orbits of excited ions. The performance characteristics of the NADEL ICR cell are comparable with the state-of-the-art FT-ICR MS implementations for small molecule, peptide, protein, and petroleomics analyses. In addition, the NADEL ICR cell's design improves the flexibility of ICR cells and facilitates implementation of advanced capabilities (e.g., quadrupolar ion detection for improved mainstream applications). It also creates an intriguing opportunity for addressing the major bottleneck in FTMS-increasing its throughput via simultaneous acquisition of multiple transients or via generation of periodic non-sinusoidal transient signals.

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Fine Structure in Isotopic Peak Distributions Measured Using a Dynamically Harmonized Fourier Transform Ion Cyclotron Resonance Cell at 7 T

Cited by 64 publications

References 5 publications

Tracking the Magnetron Motion in FT-ICR Mass Spectrometry

Tracking the Magnetron Motion in FT-ICR Mass Spectrometry

Platform Dependencies in Bottom-up Hydrogen/Deuterium Exchange Mass Spectrometry

Ion Trap with Narrow Aperture Detection Electrodes for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

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