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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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DeGraan-Weber N, Zhao B, Reilly JP. Unusual fragmentation of derivatized cysteine-containing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1491-1496. [PMID: 29874404 PMCID: PMC6430700 DOI: 10.1002/rcm.8196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Modification of cysteines by aminoethylation results in side chains similar to those of lysine. Trypsin cleaves at this modified residue and this labeling method can facilitate the analysis of proteins, specifically antibodies. In this work, the ability to identify peptides containing aminoethylated cysteines is investigated through digestion, covalent labeling, and low-energy ion fragmentation. METHODS A prototype antibody was reduced, aminoethylated, and digested with either Lys-N or Glu-C. The resulting peptides were amidinated with SMTA and analyzed by PSD in a MALDI-TOF/TOF mass spectrometer or by CID in an ESI ion trap/orbitrap mass spectrometer. RESULTS PSD and CID fragmentation of peptides with an amidinated aminoethylated cysteine can produce an intense characteristic loss from this modified residue. A neutral loss of 118 Da or charged loss of 119 Da is observed when peptides have low charges. This fragment can form when the cysteine is located in any position in the peptide. The rationalization for this ion is that the amidino group can be initially neutral or protonated and initiates fragmentation. CONCLUSIONS The combination of a dual-labeling technique and low-energy fragmentation produces an abundant diagnostic ion for the analysis of cysteine-containing peptides. These 118 and 119 Da losses are observed when protons are sequestered.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
| | - Bingqing Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
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DeGraan-Weber N, Ward SA, Reilly JP. A Novel Triethylphosphonium Charge Tag on Peptides: Synthesis, Derivatization, and Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1889-1900. [PMID: 28560565 PMCID: PMC5709245 DOI: 10.1007/s13361-017-1694-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 06/07/2023]
Abstract
Charge tagging is a peptide derivatization process that commonly localizes a positive charge on the N-terminus. Upon low energy activation (e.g., collision-induced dissociation or post-source decay) of charge tagged peptides, relatively few fragment ions are produced due to the absence of mobile protons. In contrast, high energy fragmentation, such as 157 nm photodissociation, typically leads to a series of a-type ions. Disadvantages of existing charge tags are that they can produce mobile protons or that they are undesirably large and bulky. Here, we investigate a small triethylphosphonium charge tag with two different linkages: amide (158 Da) and amidine bonds (157 Da). Activation of peptides labeled with a triethylphosphonium charge tag through an amide bond can lead to loss of the charge tag and the production of protonated peptides. This enables low intensity fragment ions from both the protonated and charge tagged peptides to be observed. Triethylphosphonium charge tagged peptides linked through an amidine bond are more stable. Post-source decay and photodissociation yield product ions that primarily contain the charge tag. Certain amidine induced fragments are also observed. The previously reported tris(trimethoxyphenyl) phosphonium acetic acid N-hydroxysuccinimidyl ester charge tag shows a similar fragment ion distribution, but the mass of the triethylphosphonium tag label is 415 Da smaller. Graphical Abstract ᅟ.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Sarah A Ward
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, 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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Brodbelt JS. Photodissociation mass spectrometry: new tools for characterization of biological molecules. Chem Soc Rev 2014; 43:2757-83. [PMID: 24481009 PMCID: PMC3966968 DOI: 10.1039/c3cs60444f] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.
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Webber N, He Y, Reilly JP. 157 nm photodissociation of dipeptide ions containing N-terminal arginine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:196-203. [PMID: 24310819 DOI: 10.1007/s13361-013-0762-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
Twenty singly-charged dipeptide ions with N-terminal arginine were photodissociated using 157 nm light in both a linear ion-trap mass spectrometer and a MALDI-TOF-TOF mass spectrometer. Analogous to previous work on dipeptides containing C-terminal arginine, this set of samples enabled insights into the photofragmentation propensities associated with individual residues. In addition to familiar products such as a-, d-, and immonium ions, m2 and m2+13 ions were also observed. Certain side chains tended to cleave between their β and γ carbons without necessarily forming d- or w-type ions, and a few other ions were produced by the high-energy fragmentation of multiple bonds.
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Affiliation(s)
- Nathaniel Webber
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
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