Phase Correction for Absorption Mode Two-Dimensional Mass Spectrometry

Delsuc, Marc-André; Breuker, Kathrin; Agthoven, Maria A. van

doi:10.3390/molecules26113388

Cited by 3 publications

(7 citation statements)

References 55 publications

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“…Figure a shows the 2D mass spectrum of the [M+6H] 6+ ions of the equimolar mixture of K7 Ac and K16 3m with a frequency range of 10 kHz in phase-corrected absorption mode. A previous study has shown that the isotopic pattern of [M+6H] 6+ ions of methylated histone peptides is baseline-resolved in the vertical precursor ion dimension . The frequency difference between two adjacent data points (or resolution) in the vertical dimension is 4.9 Hz.…”

Section: Resultsmentioning

confidence: 99%

“…A previous study has shown that the isotopic pattern of [M+6H] 6+ ions of methylated histone peptides is baselineresolved in the vertical precursor ion dimension. 34 The frequency difference between two adjacent data points (or resolution) in the vertical dimension is 4.9 Hz. Moreover, the maximum value of t 1 in this experiment is 51.2 ms, which means that the minimum frequency resolution of each peak is 19.5 Hz.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…The 1D mass spectra were apodized with a square sine-bell window with a maximum at 0.15 and zero-filled to 4096 data points before Fourier transformation and quadratic phase-correction and baseline correction. The 2D mass spectra were digitally demodulated, apodized with a sine-bell window with a maximum at 0.15, zero-filled twice, denoised with the SANE algorithm (with a rank of 30), and phase-corrected quadratically along the horizontal axis and linearly along the vertical access, before the frequencies were offset to recalculate the original frequency range in the vertical dimension. ,,, The size of the resulting data sets was 1,048,576 data points horizontally (fragment ion dimension) by 2048 data points vertically (precursor ion dimension).…”

Section: Experimental Methodsmentioning

confidence: 99%

“…The pulse sequence for 2D FT-ICR MS (two-dimensional Fourier transform ion cyclotron resonance mass spectrometry) was developed by Pfändler et al and has been optimized for various fragmentation methods, such as infrared multiphoton dissociation, electron capture dissociation (ECD), infrared-activated ECD, electron-induced dissociation, and ultraviolet dissociation. − Programs have been developed for data processing and analysis, and algorithms have been developed for noise reduction. ,− Applications for 2D MS include small molecules, proteomics (bottom-up and top-down), polymer analysis, and agrochemicals. ,,− A narrowband method has been developed for high resolution precursor-fragment correlation over small m / z ranges as well as strategies for phase correction to improve both the resolving power and the signal-to-noise ratio of 2D mass spectra. − …”

Section: Introductionmentioning

confidence: 99%

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Ultra-Accurate Correlation between Precursor and Fragment Ions in Two-Dimensional Mass Spectrometry: Acetylated vs Trimethylated Histone Peptides

Palasser

Heel

Delsuc

et al. 2023

J. Am. Soc. Mass Spectrom.

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Two-dimensional mass spectrometry (2D MS) is a method for tandem mass spectrometry in which precursor and fragment ions are correlated by manipulating ion radii rather than by ion isolation. A 2D mass spectrum contains the fragmentation patterns of all analytes in a sample, acquired in parallel. We report ultrahigh-resolution narrowband 2D mass spectra of a mixture of two histone peptides with the same sequence, one of which carries an acetylation and the other a trimethylation (m/z 0.006 difference). We reduced the distance between data points in the precursor ion dimension and compared the accuracy of the precursor-fragment correlation with the resolving power. We manage to perform label-free quantification on the histone peptide mixture and show that precursor and fragment ions can be accurately correlated even though the precursor ions are not resolved. Finally, we show that increasing the resolution of a 2D mass spectrum in the precursor ion dimension too far can lead to a decline in the signal-to-noise ratio.

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Section: Resultsmentioning

confidence: 99%

Section: ■ Results and Discussionmentioning

confidence: 99%

Section: Experimental Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Ultra-Accurate Correlation between Precursor and Fragment Ions in Two-Dimensional Mass Spectrometry: Acetylated vs Trimethylated Histone Peptides

Palasser

Heel

Delsuc

et al. 2023

J. Am. Soc. Mass Spectrom.

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“…This technique has been applied with a variety of dissociation methods for the analysis of ubiquitin and IgG antibodies, via top-down and bottom-up approaches. Although the data provided by 2D MS has much higher resolution, − the analysis and data processing time are significantly longer.…”

Section: Introductionmentioning

confidence: 99%

Machine-Learning Classification of Bacteria Using Two-Dimensional Tandem Mass Spectrometry

Gonzalez,

Snyder,

Casey

et al. 2023

Anal. Chem.

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Biothreat detection has continued to gain attention. Samples suspected to fall into any of the CDC's biothreat categories require identification by processes that require specialized expertise and facilities. Recent developments in analytical instrumentation and machine learning algorithms offer rapid and accurate classification of Gram-positive and Gramnegative bacterial species. This is achieved by analyzing the negative ions generated from bacterial cell extracts with a modified linear quadrupole ion-trap mass spectrometer fitted with twodimensional tandem mass spectrometry capabilities (2D MS/MS). The 2D MS/MS data domain of a bacterial cell extract is recorded within five s using a five-scan average after sample preparation by a simple extraction. Bacteria were classified at the species level by their lipid profiles using the random forest, k-nearest neighbor, and multilayer perceptron machine learning models. 2D MS/MS data can also be treated as image data for use with image recognition algorithms such as convolutional neural networks. The classification accuracy of all models tested was greater than 99%. Adding to previously published work on the 2D MS/MS analysis of bacterial growth and the profiling of sporulating bacteria, this study demonstrates the utility and information-rich nature of 2D MS/MS in the identification of bacterial pathogens at the species level when coupled with machine learning.

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Top-Down Proteoform Analysis by 2D MS with Quadrupolar Detection

Polák,

Palasser,

Kádek

et al. 2023

Anal. Chem.

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Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that does not rely on ion isolation to correlate the precursor and fragment ions. On a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), 2D MS instead uses the modulation of precursor ion radii inside the ICR cell before fragmentation and yields 2D mass spectra that show the fragmentation patterns of all the analytes. In this study, we perform 2D MS for the first time with quadrupolar detection in a dynamically harmonized ICR cell. We discuss the advantages of quadrupolar detection in 2D MS and how we adapted existing data processing techniques for accurate frequency-to-mass conversion. We apply 2D MS with quadrupolar detection to the top-down analysis of covalently labeled ubiquitin with ECD fragmentation, and we develop a workflow for label-free relative quantification of biomolecule isoforms in 2D MS.

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Phase Correction for Absorption Mode Two-Dimensional Mass Spectrometry

Cited by 3 publications

References 55 publications

Ultra-Accurate Correlation between Precursor and Fragment Ions in Two-Dimensional Mass Spectrometry: Acetylated vs Trimethylated Histone Peptides

Ultra-Accurate Correlation between Precursor and Fragment Ions in Two-Dimensional Mass Spectrometry: Acetylated vs Trimethylated Histone Peptides

Machine-Learning Classification of Bacteria Using Two-Dimensional Tandem Mass Spectrometry

Top-Down Proteoform Analysis by 2D MS with Quadrupolar Detection

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