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Schneider P, Keller P, Schubert I, Bender M, Trautmann C, Dürr M. Bond-specific fragmentation of oligopeptides via electronic stopping of swift heavy ions in molecular films. Sci Rep 2022; 12:17975. [PMID: 36289262 PMCID: PMC9605986 DOI: 10.1038/s41598-022-21744-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/30/2022] [Indexed: 01/24/2023] Open
Abstract
Highly bond-specific fragmentation of oligopeptides induced by swift heavy ion (SHI) irradiation was investigated by means of mass spectrometry. In pronounced contrast to measurements of samples irradiated with keV ions, oligopeptides which were exposed to 946 MeV Au ions show a high abundance of specific fragments. The highly bond-specific nature of SHI-induced fragmentation is attributed to electronic stopping as the most relevant energy loss mechanism for SHI in the oligopeptide samples in combination with the subsequent coupling between the excited electronic and the atomic subsystem. Fragmentation induced by SHI is observed to be further influenced by the structure of the oligopeptides, suggesting that electronic excitation and/or the electronic-vibrational coupling depend on the details of the molecular structure.
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Affiliation(s)
- P. Schneider
- grid.8664.c0000 0001 2165 8627Institut für Angewandte Physik and Zentrum für Materialforschung, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - P. Keller
- grid.8664.c0000 0001 2165 8627Institut für Angewandte Physik and Zentrum für Materialforschung, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - I. Schubert
- grid.159791.20000 0000 9127 4365GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstrasse 1, 64291 Darmstadt, Germany
| | - M. Bender
- grid.159791.20000 0000 9127 4365GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstrasse 1, 64291 Darmstadt, Germany ,grid.449475.f0000 0001 0669 6924Fachbereich Ingenieurwissenschaften, Hochschule RheinMain, Kurt-Schumacher-Ring 18, 65197 Wiesbaden, Germany
| | - C. Trautmann
- grid.159791.20000 0000 9127 4365GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstrasse 1, 64291 Darmstadt, Germany ,grid.6546.10000 0001 0940 1669Fachbereich Materialwissenschaften, Technische Universität Darmstadt, Alarich-Weiss-Strasse 2, 64287 Darmstadt, Germany
| | - M. Dürr
- grid.8664.c0000 0001 2165 8627Institut für Angewandte Physik and Zentrum für Materialforschung, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
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Dilillo M, de Graaf EL, Yadav A, Belov ME, McDonnell LA. Ultraviolet Photodissociation of ESI- and MALDI-Generated Protein Ions on a Q-Exactive Mass Spectrometer. J Proteome Res 2018; 18:557-564. [PMID: 30484663 DOI: 10.1021/acs.jproteome.8b00896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The identification of molecular ions produced by MALDI or ESI strongly relies on their fragmentation to structurally informative fragments. The widely diffused fragmentation techniques for ESI multiply charged ions are either incompatible (ECD and ETD) or show lower efficiency (CID, HCD), with the predominantly singly charged peptide and protein ions formed by MALDI. In-source decay has been successfully adopted to sequence MALDI-generated ions, but it further increases spectral complexity, and it is not compatible with mass-spectrometry imaging. Excellent UVPD performances, in terms of number of fragment ions and sequence coverage, has been demonstrated for electrospray ionization for multiple proteomics applications. UVPD showed a much lower charge-state dependence, and so protein ions produced by MALDI may exhibit equal propensity to fragment. Here we report UVPD implementation on an Orbitrap Q-Exactive Plus mass spectrometer equipped with an ESI/EP-MALDI. UVPD of MALDI-generated ions was benchmarked against MALDI-ISD, MALDI-HCD, and ESI-UVPD. MALDI-UVPD outperformed MALDI-HCD and ISD, efficiently sequencing small proteins ions. Moreover, the singly charged nature of MALDI-UVPD avoids the bioinformatics challenges associated with highly congested ESI-UVPD mass spectra. Our results demonstrate the ability of UVPD to further improve tandem mass spectrometry capabilities for MALDI-generated protein ions. Data are available via ProteomeXchange with identifier PXD011526.
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Affiliation(s)
- Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy
| | - Erik L de Graaf
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy
| | - Avinash Yadav
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy.,Scuola Normale Superiore di Pisa , 56126 Pisa , Italy
| | - Mikhail E Belov
- Spectroglyph LLC , Kennewick , Washington 99338 , United States
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy.,Center for Proteomics and Metabolomics , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
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Li H, Sheng Y, McGee W, Cammarata M, Holden D, Loo JA. Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry. Anal Chem 2017; 89:2731-2738. [PMID: 28192979 DOI: 10.1021/acs.analchem.6b02377] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) has played an increasingly important role in the identification and structural and functional characterization of proteins. In particular, the use of tandem mass spectrometry has afforded one of the most versatile methods to acquire structural information for proteins and protein complexes. The unique nature of electron capture dissociation (ECD) for cleaving protein backbone bonds while preserving noncovalent interactions has made it especially suitable for the study of native protein structures. However, the intra- and intermolecular interactions stabilized by hydrogen bonds and salt bridges can hinder the separation of fragments even with preactivation, which has become particularly problematic for the study of large macromolecular proteins and protein complexes. Here, we describe the capabilities of another activation method, 30 eV electron ionization dissociation (EID), for the top-down MS characterization of native protein-ligand and protein-protein complexes. Rich structural information that cannot be delivered by ECD can be generated by EID. EID allowed for the comparison of the gas-phase and the solution-phase structural stability and unfolding process of human carbonic anhydrase I (HCA-I). In addition, the EID fragmentation patterns reflect the structural similarities and differences among apo-, Zn-, and Cu,Zn-superoxide dismutase (SOD1) dimers. In particular, the structural changes due to Cu-binding and a point mutation (G41D) were revealed by EID-MS. The performance of EID was also compared to that of 193 nm ultraviolet photodissociation (UVPD), which allowed us to explore their qualitative similarities and differences as potential valuable tools for the MS study of native proteins and protein complexes.
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Affiliation(s)
- Huilin Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States
| | - Yuewei Sheng
- Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California , Los Angeles, California 90095, United States
| | - William McGee
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Michael Cammarata
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Dustin Holden
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California , Los Angeles, California 90095, United States
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light‐Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dustin D. Holden
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH Hanna-Kunath-Strasse 11 28199 Bremen Germany
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - James D. Sanders
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - Jennifer S. Brodbelt
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light-Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016; 55:12417-21. [PMID: 27605434 DOI: 10.1002/anie.201605850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/02/2016] [Indexed: 11/09/2022]
Abstract
The first application of light-emitting diodes (LEDs) for ultraviolet photodissociation (UVPD) mass spectrometry is reported. LEDs provide a compact, low cost light source and have been incorporated directly into the trapping cell of an Orbitrap mass spectrometer. MS/MS efficiencies of over 50 % were obtained using an extended irradiation period, and UVPD was optimized by modulating the ion trapping parameters to maximize the overlap between the ion cloud and the irradiation volume.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199, Bremen, Germany
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA.
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Morrison LJ, Rosenberg JA, Singleton JP, Brodbelt JS. Statistical Examination of the a and a + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1443-53. [PMID: 27206509 PMCID: PMC4974117 DOI: 10.1007/s13361-016-1418-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/01/2016] [Accepted: 05/06/2016] [Indexed: 05/11/2023]
Abstract
Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Jake A Rosenberg
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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Hoffmann WD, Jackson GP. Charge transfer dissociation (CTD) mass spectrometry of peptide cations using kiloelectronvolt helium cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1939-43. [PMID: 25231159 DOI: 10.1007/s13361-014-0989-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/23/2014] [Accepted: 07/27/2014] [Indexed: 05/04/2023]
Abstract
A kiloelectronvolt beam of helium ions is used to ionize and fragment precursor peptide ions starting in the 1+ charge state. The electron affinity of helium cations (24.6 eV) exceeds the ionization potential of protonated peptides and can therefore be used to abstract an electron from--or charge exchange with--the isolated precursor ions. Kiloelectronvolt energies are used, (1) to overcome the Coulombic repulsion barrier between the cationic reactants, (2) to overcome ion-defocussing effects in the ion trap, and (3) to provide additional activation energy. Charge transfer dissociation (CTD) of the [M+H](+) precursor of Substance P gives product ions such as [M+H](2+•) and a dominant series of a ions in both the 1+ and 2+ charge states. These observations, along with the less-abundant a + 1 ions, are consistent with ultraviolet photodissociation (UVPD) results of others and indicate that C-C(α) cleavages are possible through charge exchange with helium ions. Although the efficiencies and timescale of CTD are not yet suitable for on-line chromatography, this new approach to ion activation provides an additional potential tool for the interrogation of gas phase ions.
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Affiliation(s)
- William D Hoffmann
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506, USA
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