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

Palasser, Michael; Heel, Sarah Viola; Delsuc, Marc-André; Breuker, Kathrin; Agthoven, Maria A. van

doi:10.1021/jasms.2c00319

Cited by 2 publications

(4 citation statements)

References 52 publications

(99 reference statements)

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“…Each plot combines the peak assignments for all charge states (7–10+) with M/K acetylation sites assigned by FAST-MS. These plots allow us to locate acetylation sites and quantify the extent of acetylation. − …”

Section: Resultsmentioning

confidence: 99%

“…2D MS has been applied to the analysis of small molecules, agrochemicals, polymers, and protein tryptic digests and the top-down analysis of proteins. − 2D MS has also been used for the label-free relative quantification of modified peptides in a proof-of-concept study. − One application of label-free quantification by 2D MS is the top-down analysis of covalently labeled proteins.…”

Section: Introductionmentioning

confidence: 99%

“… 26 − 29 2D MS has also been used for the label-free relative quantification of modified peptides in a proof-of-concept study. 30 − 32 One application of label-free quantification by 2D MS is the top-down analysis of covalently labeled proteins.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Polák,

Palasser,

Kádek

et al. 2023

Anal. Chem.

Self Cite

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

Cited by 2 publications

References 52 publications

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

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

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

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