The spontaneous loss of coherence catastrophe in fourier transform ion cyclotron resonance mass spectrometry

Aizikov, Konstantin; Mathur, Raman; O’Connor, Peter B.

doi:10.1016/j.jasms.2008.09.028

Cited by 29 publications

(39 citation statements)

References 94 publications

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“…Aizikov et al [38] describe this phenomenon as a spontaneous loss of coherence catastrophe (SLCC). They noted that Nikolaev et al [14] also observed this phenomenon in their simulation.…”

Section: ϫ3mentioning

confidence: 99%

Peak coalescence, spontaneous loss of coherence, and quantification of the relative abundances of two species in the plasma regime: Particle-in-cell modeling of fourier transform ion cyclotron resonance mass spectrometry

Nakata

Hart

Peterson

2010

J. Am. Soc. Mass Spectrom.

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Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is often limited by space-charge effects. Previously, particle-in-cell (PIC) simulations have been used to understand these effects on FTICR-MS signals. However, none have extended fully into the space-charge dominated (plasma) regime. We use a two-dimensional (2-D) electrostatic PIC code, which facilitates work at very high number densities at modest computational cost to study FTICR-MS in the plasma regime. In our simulation, we have observed peak coalescence and the rapid loss of signal coherence, two common experimental problems. This demonstrates that a 2-D model can simulate these effects. The 2-D code can handle a larger numbers of particles and finer spatial resolution than can currently be addressed by 3-D models. The PIC method naturally takes into account image charge and space charge effects in trapped-ion mass spectrometry. We found we can quantify the relative abundances of two closely spaced (such as 7 Be ϩ and 7 Li ϩ ) species in the plasma regime even when their peaks have coalesced. We find that the frequency of the coalesced peak shifts linearly according to the relative abundances of these species. Space charge also affects more widely spaced lines. Singlyionized 7 BeH and 7 Li have two separate peaks in the plasma regime. Both the frequency and peak area vary nonlinearly with their relative abundances. Under some conditions, the signal exhibited a rapid loss of coherence. We found that this is due to a high order diocotron instability growing in the ion cloud. (J

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“…Aizikov et al [38] describe this phenomenon as a spontaneous loss of coherence catastrophe (SLCC). They noted that Nikolaev et al [14] also observed this phenomenon in their simulation.…”

Section: ϫ3mentioning

confidence: 99%

Peak coalescence, spontaneous loss of coherence, and quantification of the relative abundances of two species in the plasma regime: Particle-in-cell modeling of fourier transform ion cyclotron resonance mass spectrometry

Nakata

Hart

Peterson

2010

J. Am. Soc. Mass Spectrom.

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“…This is clearly evident when studying the scientific publications dedicated to this technology. There have been many papers reporting technical FTMS problems and ways to alleviate or even solve them . The limited number of direct users, but also the involved technical and mathematical complexity, were probably the reasons why most of these papers were not widely read outside of the FTMS community.…”

mentioning

confidence: 99%

Accuracy of relative isotopic abundance and mass measurements in a single‐stage orbitrap mass spectrometer

Kaufmann¹,

Walker²

2012

Rapid Comm Mass Spectrometry

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Orbitrap technology offers a combination of different technical specifications which have not yet been achieved by other high-resolution mass spectrometry instrumentation. This refers to the combination of sensitivity, dynamic range, mass accuracy, resolution and speed. The high stability of the mass axis and the general ease of use made the orbitrap instrumentation attractive for routine laboratories. However, there are circumstances where significantly deviating relative isotopic abundance (RIA) and shifting accurate masses can be observed. RIA becomes biased at low ion counts. Furthermore, two adjacent, only partially resolved near-isobaric ions are detected with a deviating RIA. The presence of a very intensive mass peak does not only induce Fourier transformation related artefacts (side-lobes) but can cause mass shifts of small adjacent near-isobaric mass peaks. These effects are not as drastic as known for Fourier transform ion cyclotron resonance instruments. Still, users trying to identify or quantify trace level compounds should be aware about such limitations in order to avoid possible pitfalls.

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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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The spontaneous loss of coherence catastrophe in fourier transform ion cyclotron resonance mass spectrometry

Cited by 29 publications

References 94 publications

Peak coalescence, spontaneous loss of coherence, and quantification of the relative abundances of two species in the plasma regime: Particle-in-cell modeling of fourier transform ion cyclotron resonance mass spectrometry

Peak coalescence, spontaneous loss of coherence, and quantification of the relative abundances of two species in the plasma regime: Particle-in-cell modeling of fourier transform ion cyclotron resonance mass spectrometry

Accuracy of relative isotopic abundance and mass measurements in a single‐stage orbitrap mass spectrometer

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

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