Use of Fourier Transform for Deconvolution of the Unresolved Envelope Observed in Electrospray Ionization Mass Spectrometry of Strongly Ionic Synthetic Polymers

Prebyl, Benjamin S.; Cook, Kelsey D.

doi:10.1021/ac0348266

Cited by 13 publications

(16 citation statements)

References 26 publications

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“…Prediction of the change in the isotope cluster due to enrichment leads to identification of enriched molecules, a method on which mass spectrometric quantification and quantitative proteomic discovery relies [4–13]. Finally, accurate calculation of the isotope cluster may enable better Fourier transform deconvolution schemes for complex electrospray envelopes of macromolecules [14–18]. …”

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confidence: 99%

Calculation of the isotope cluster for polypeptides by probability grouping

Olson

Yergey

2009

J. Am. Soc. Mass Spectrom.

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This paper presents a novel theoretical basis for accurately calculating the isotope cluster of polypeptides. In contrast to previous approaches to this problem, which consider exhaustive or near exhaustive combinations of isotopic species, the program, Neutron Cluster, groups probabilities to yield highly accurate information without elucidating any fine structure within a nominal mass unit. This is a fundamental difference from any previously described algorithm for calculating the isotope cluster. As a result of this difference, the accurate isotope clusters for high molecular weight polypeptides can be calculated rapidly without any pruning. When applied to isotope enriched polypeptides, the algorithm introduces “grouping error”, which is described, quantified, and avoided by using probability partitioning.

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confidence: 99%

Calculation of the isotope cluster for polypeptides by probability grouping

Olson

Yergey

2009

J. Am. Soc. Mass Spectrom.

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“…As a demonstration of this limitation, shown in Figure are the mass spectrum and corresponding Fourier spectrum of two polydisperse samples exhibiting the problem described above: Highly sodiated anthrax lethal factor N‐terminal subunit (LFn, Figure A) and long‐chain (∼10 kDa average molecular weight, as reported by the manufacturer) polyethylene glycol (“PEG 10k”) polymer (Figure B). While Fourier transformation of the mass spectrum facilitates sodium adduct and polymer subunit mass determination using previously described methods,, it is difficult to uniquely identify charge states for both analytes (LFn and the long‐chain polymer ions) in the Fourier spectrum due to the presence of many other peaks. Without confident charge state determination, determining accurate mass information for these ions from either the mass spectrum or Fourier spectrum is very difficult.…”

Section: Figurementioning

confidence: 99%

Liberating Native Mass Spectrometry from Dependence on Volatile Salt Buffers by Use of Gábor Transform

Cleary

Prell

2019

ChemPhysChem

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Volatile salts, such as ammonium acetate, are commonly used in buffers for the analysis of intact proteins and protein complexes in native electrospray ionization mass spectrometry. Although these solutions are not technically buffers near pH 7, the volatile nature of the salt minimizes ion adduction to proteins upon transfer to vacuum. Conversely, common biochemical salt buffers, such as Tris/NaCl, are not traditionally used in native mass spectrometry because of the tendency of sodium and other ions to adduct to proteins or form large cluster ions, severely frustrating accurate mass assignment. Here, we demonstrate a Gábor transform method for extracting signal from native-like protein ions even in the presence of a large salt-cluster background. We further show the utility of this method in characterizing polymers and show that the measured average mass of long-chain polyethylene glycol ions from a commercial polymer sample is~30 % higher than the manufacturer-estimated average mass. It is expected that this method will enable more widespread use of conventional biochemical buffers in native mass spectrometry and decrease dependence on volatile salts.

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“…The principle of the Fourier Transform (FT)-based mass spectrum analysis method used here for deconvolving heterogeneous mass populations was previously described in detail [25, 45, 46] and therefore will only be briefly explained here. The key concept to the FT algorithm is that a distribution of mass spectral peaks for an individual charge state z of an analyte containing various numbers of a repeated subunit with mass m s can be described as a comb of equally-spaced peaks multiplied by a mass spectral envelope function.…”

Section: Theorymentioning

confidence: 99%

“…It can thus be highly advantageous to have accurate estimates of these parameters before implementing the algorithms in order to obtain reliable results. Alternatively, Fourier Transform-based deconvolution approaches require minimal data processing and parameter guessing [25, 45, 46]. For example, the recently introduced program iFAMS (interactive Fourier-Transform Analysis for Mass Spectrometry) requires only linear data interpolation and specification of the minimum allowed number of data points separating frequency-domain peaks [25].…”

Section: Introductionmentioning

confidence: 99%

Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics

Cleary

Bagal

et al. 2018

J. Am. Soc. Mass Spectrom.

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Native mass spectra of large, polydisperse biomolecules with repeated subunits, such as lipoprotein Nanodiscs, can often be challenging to analyze by conventional methods. The presence of tens of closely spaced, overlapping peaks in these mass spectra can make charge state, total mass, or subunit mass determinations difficult to measure by traditional methods. Recently, we introduced a Fourier Transform-based algorithm that can be used to deconvolve highly congested mass spectra for polydisperse ion populations with repeated subunits and facilitate identification of the charge states, subunit mass, charge-state-specific, and total mass distributions present in the ion population. Here, we extend this method by investigating the advantages of using overtone peaks in the Fourier spectrum, particularly for mass spectra with low signal-to-noise and poor resolution. This method is illustrated for lipoprotein Nanodisc mass spectra acquired on three common platforms, including the first reported native mass spectrum of empty "large" Nanodiscs assembled with MSP1E3D1 and over 300 noncovalently associated lipids. It is shown that overtone peaks contain nearly identical stoichiometry and charge state information to fundamental peaks but can be significantly better resolved, resulting in more reliable reconstruction of charge-state-specific mass spectra and peak width characterization. We further demonstrate how these parameters can be used to improve results from Bayesian spectral fitting algorithms, such as UniDec. Graphical Abstract ᅟ.

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Use of Fourier Transform for Deconvolution of the Unresolved Envelope Observed in Electrospray Ionization Mass Spectrometry of Strongly Ionic Synthetic Polymers

Cited by 13 publications

References 26 publications

Calculation of the isotope cluster for polypeptides by probability grouping

Calculation of the isotope cluster for polypeptides by probability grouping

Liberating Native Mass Spectrometry from Dependence on Volatile Salt Buffers by Use of Gábor Transform

Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics

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