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Le MT, Holden DT, Manheim JM, Dziekonski ET, Iyer K, Graham Cooks R. Two-Dimensional Tandem Mass Spectrometry for Biopolymer Structural Analysis. Angew Chem Int Ed Engl 2024; 63:e202315904. [PMID: 38117612 DOI: 10.1002/anie.202315904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 12/22/2023]
Abstract
Biopolymer analysis, including proteomics and glycomics, relies heavily on the use of mass spectrometry for structural elucidation, including sequence determination. Novel methods to improve sample workup, instrument performance, and data analysis continue to be developed to address shortcomings associated with sample preparation, analysis time, data quality, and data interpretation. Here, we present a new method that couples in-source collision-induced dissociation (IS-CID) with two-dimensional tandem mass spectrometry (2D MS/MS) as a way to simplify proteomics and glycomics workflows while also providing additional insight into analyte structures over traditional MS/MS experiments. Specifically, IS-CID is employed as a gas-phase digestion method, i.e., to break down intact full-length polysaccharide or peptide ions prior to mass analysis. The resulting mixtures of oligomeric ions are analyzed by 2D-MS/MS, a technique that allows association of product ions with their precursor ions without isolation of the latter. A novel data analysis strategy is introduced to leverage the second dimension of 2D MS/MS spectra, in which stairstep patterns, representing outputs of a molecule's MSn scans, are extracted for structural interconnectivity information on the oligomer. The results demonstrate the potential applicability of 2D MS/MS strategies to the modern omics workflow and structural analysis of various classes of biopolymers.
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Affiliation(s)
- MyPhuong T Le
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Dylan T Holden
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Jeremy M Manheim
- Merck & Co., Inc., Analytical Research and Development, Rahway, NJ 07065, USA
| | - Eric T Dziekonski
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Kiran Iyer
- Merck & Co., Inc., Analytical Research and Development, Rahway, NJ 07065, USA
| | - R Graham Cooks
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
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2
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Ivanova B. Special Issue with Research Topics on "Recent Analysis and Applications of Mass Spectra on Biochemistry". Int J Mol Sci 2024; 25:1995. [PMID: 38396673 PMCID: PMC10888122 DOI: 10.3390/ijms25041995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Analytical mass spectrometry applies irreplaceable mass spectrometric (MS) methods to analytical chemistry and chemical analysis, among other areas of analytical science [...].
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
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3
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Gonzalez LE, Snyder DT, Casey H, Hu Y, Wang DM, Guetzloff M, Huckaby N, Dziekonski ET, Wells JM, Cooks RG. Machine-Learning Classification of Bacteria Using Two-Dimensional Tandem Mass Spectrometry. Anal Chem 2023; 95:17082-17088. [PMID: 37937965 DOI: 10.1021/acs.analchem.3c04016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
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 Gram-negative 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 two-dimensional 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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Affiliation(s)
- L Edwin Gonzalez
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| | - Dalton T Snyder
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - Harman Casey
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - Yanyang Hu
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| | - Donna M Wang
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| | - Megan Guetzloff
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - Nicole Huckaby
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - Eric T Dziekonski
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| | - J Mitchell Wells
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
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4
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Palasser M, Heel SV, Delsuc MA, Breuker K, van Agthoven MA. Ultra-Accurate Correlation between Precursor and Fragment Ions in Two-Dimensional Mass Spectrometry: Acetylated vs Trimethylated Histone Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:608-616. [PMID: 36930827 PMCID: PMC10080674 DOI: 10.1021/jasms.2c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/23/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
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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Affiliation(s)
- Michael Palasser
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Sarah V. Heel
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Marc-André Delsuc
- Institut
de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, UMR 7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
- CASC4DE, Pôle API, 300 Bd. Sébastien
Grant, 67400 Illkirch-Graffenstaden, France
| | - Kathrin Breuker
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Maria A. van Agthoven
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
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5
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Gonzalez LE, Szalwinski LJ, Sams TC, Dziekonski ET, Cooks RG. Metabolomic and Lipidomic Profiling of Bacillus Using Two-Dimensional Tandem Mass Spectrometry. Anal Chem 2022; 94:16838-16846. [DOI: 10.1021/acs.analchem.2c03961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- L. Edwin Gonzalez
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lucas J. Szalwinski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Thomas C. Sams
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Eric T. Dziekonski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - R. Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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6
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Szalwinski LJ, Gonzalez LE, Morato NM, Marsh BM, Cooks RG. Bacterial growth monitored by two-dimensional tandem mass spectrometry. Analyst 2022; 147:940-946. [PMID: 35166732 DOI: 10.1039/d1an01901e] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The growth of the bacterium E. coli was monitored by targeting the phospholipid constituents through desorption electrospray ionization and characterizing individual sets of isomers by recording the full 2D MS/MS data domain in a single scan of a modified quadrupole ion trap mass spectrometer. The experiments tested the applicability of the new instrumental capabilities which include sample interrogation at the molecular level for multiple components at speeds of <10 seconds/sample. The major lipids observed were phosphatidylethanolamines and phosphatidylglycerols and the growth experiment showed fatty acid chain modification from alkene to cyclopropyl groups over time. Notably, these novel MS scans were also performed using desorption electrospray ionization (DESI) to quickly sample complex mixtures without pre-separation. This demonstration experiment has implications for the value of ambient ionization mass spectrometry for monitoring biological systems on physiologically relevant timescales.
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Affiliation(s)
- Lucas J Szalwinski
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
| | - L Edwin Gonzalez
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Nicolás M Morato
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Brett M Marsh
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
| | - R Graham Cooks
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
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7
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Szalwinski LJ, Hu Y, Morato NM, Cooks RG, Salentijn GI. Novel Ion Trap Scan Modes to Develop Criteria for On-Site Detection of Sulfonamide Antibiotics. Anal Chem 2021; 93:13904-13911. [PMID: 34617742 PMCID: PMC8529578 DOI: 10.1021/acs.analchem.1c02790] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Advances in ambient
ionization techniques have facilitated the
direct analysis of complex mixtures without sample preparation. Significant
attention has been given to innovating ionization methods so that
multiple options are now available, allowing for ready selection of
the best methods for particular analyte classes. These ambient techniques
are commonly implemented on benchtop systems, but their potential
application with miniature mass spectrometers for in situ measurements is even more powerful. These applications require that
attention be paid to tailoring the mass spectrometric methodology
for the on-site operation. In this study, combinations of scan modes
are employed to efficiently determine what tandem mass spectrometry
(MS/MS) operations are most useful for detecting sulfonamides using
a miniature ion trap after ionization. First, mixtures of representative
sulfonamide antibiotics were interrogated using a 2D MS/MS scan on
a benchtop ion trap in order to determine which class-specific fragments
(ionic or neutral) are shared between the sulfonamides and thus have
diagnostic value. Then, three less-used combination scans were recorded:
(i) a simultaneous precursor ion scan was used to detect both analytes
and an internal standard in a single ion injection event to optimize
quantitative performance; (ii) a simultaneous precursor/neutral loss
scan was used to improve detection limits; and finally, (iii) the
simultaneous precursor/neutral loss scan was implemented in a miniature
mass spectrometer and representative sulfonamides were detected at
concentrations as low as 100 ng/mL by nano-electrospray and 0.5 ng
absolute by paper spray ionization, although improvements in the stability
of the home-built instrumentation are needed to further optimize performance.
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Affiliation(s)
- Lucas J Szalwinski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yanyang Hu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nicolás M Morato
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Gert Ij Salentijn
- Laboratory of Organic Chemistry, Wageningen University, Wageningen 6708 WE, The Netherlands.,Wageningen Food Safety Research (WFSR), Wageningen University & Research, Wageningen 6700 AE, The Netherlands
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8
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Morgan TE, Wootton CA, Marzullo B, Paris J, Kerr A, Ellacott SH, van Agthoven MA, Barrow MP, Bristow AWT, Perrier S, O'Connor PB. Characterization Across a Dispersity: Polymer Mass Spectrometry in the Second Dimension. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2153-2161. [PMID: 34264672 DOI: 10.1021/jasms.1c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Due to the natural dispersity that is present in synthetic polymers, an added complexity is always present in the analysis of polymeric species. Tandem mass spectrometry analysis requires the isolation of individual precursors before a fragmentation event to allow the unambiguous characterization of these species and is not viable at certain levels of complexity due to achievable isolation widths. Two-dimensional mass spectrometry (2DMS) fragments ions and correlates fragments with their corresponding precursors without the need for isolation. In this study, 2DMS electron capture dissociation (ECD) fragmentation of a polyoxazoline and polyacrylamide species was carried out, resulting in the analysis of byproducts and individual polymer species without the use of chromatographic techniques. This study shows that 2DMS ECD is a powerful tool for the analysis of polyacrylamide and polyoxazoline species and offers a new dimension in the characterization of polymers.
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Affiliation(s)
- Tomos E Morgan
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Christopher A Wootton
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Bryan Marzullo
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Johanna Paris
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Andrew Kerr
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Sean H Ellacott
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Maria A van Agthoven
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Anthony W T Bristow
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, United Kingdom
| | - Sebastien Perrier
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
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9
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Phase Correction for Absorption Mode Two-Dimensional Mass Spectrometry. Molecules 2021; 26:molecules26113388. [PMID: 34205070 PMCID: PMC8199897 DOI: 10.3390/molecules26113388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/03/2022] Open
Abstract
Two-dimensional mass spectrometry (2D MS) is a tandem mass spectrometry method that relies on manipulating ion motions to correlate precursor and fragment ion signals. 2D mass spectra are obtained by performing a Fourier transform in both the precursor ion mass-to-charge ratio (m/z) dimension and the fragment ion m/z dimension. The phase of the ion signals evolves linearly in the precursor m/z dimension and quadratically in the fragment m/z dimension. This study demonstrates that phase-corrected absorption mode 2D mass spectrometry improves signal-to-noise ratios by a factor of 2 and resolving power by a factor of 2 in each dimension compared to magnitude mode. Furthermore, phase correction leads to an easier differentiation between ion signals and artefacts, and therefore easier data interpretation.
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