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Kirschbaum C, Greis K, Torres-Boy A, Riedel J, Gewinner S, Schöllkopf W, Meijer G, Helden GV, Pagel K. Studying the Intrinsic Reactivity of Chromanes by Gas-Phase Infrared Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1950-1958. [PMID: 38950388 PMCID: PMC11311547 DOI: 10.1021/jasms.4c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]
Abstract
Tandem mass spectrometry is routinely used for the structural analysis of organic molecules, but many fragmentation reactions are not well understood. Because several potential structures can correspond to a measured mass, the assignment of product ions is ambiguous using mass spectrometry alone. Here, we combine mass spectrometry with high-resolution gas-phase infrared spectroscopy and computational chemistry tools to identify product ion structures and derive collision-induced fragmentation mechanisms of the chromane derivatives Trolox and Methyltrolox. We find that protonated Trolox and Methyltrolox fragment identically via dehydration and decarbonylation, while deprotonated ions display substantially diverging reactivities. For deprotonated Methyltrolox, we observe unusual radical fragmentation reactions and suggest a [1,2]-Wittig rearrangement involving aryl migration in the gas phase. Overall, the combined experimental and theoretical approach presented here revealed complex proton dynamics and intramolecular rearrangement reactions, which expand our understanding on structure-reactivity relationships of isolated molecules in different protonation states.
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Affiliation(s)
- Carla Kirschbaum
- Freie
Universität Berlin, Institute of Chemistry
and Biochemistry, 14195 Berlin, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Kim Greis
- Freie
Universität Berlin, Institute of Chemistry
and Biochemistry, 14195 Berlin, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | | | - Jerome Riedel
- Freie
Universität Berlin, Institute of Chemistry
and Biochemistry, 14195 Berlin, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Sandy Gewinner
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | | | - Gerard Meijer
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Kevin Pagel
- Freie
Universität Berlin, Institute of Chemistry
and Biochemistry, 14195 Berlin, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
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2
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Mohamed A, Rana A, Perez E, Dahlmann F, Fry A, Menges FS, van Stipdonk M, Jäger S, Boyer MA, McCoy AB, Johnson MA. Characterization of the Oxazolone and Macrocyclic Motifs in the b n ( n = 2-5) Product Ions from Collision-Induced Dissociation of Protonated Oligoglycine Peptides with Isomer-Selective, Cryogenic Vibrational Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:326-332. [PMID: 38150530 DOI: 10.1021/jasms.3c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Collision-induced dissociation (CID) of small, protonated peptides leads to the formation of b-type fragment ions that can occur with several structural motifs driven by different covalent intramolecular bonding arrangements. Here, we characterize the so-called "oxazolone" and "macrocycle" bn ion structures that occur upon CID of oligoglycine peptides (Gn) ions (n = 2-6). This is determined by acquiring the vibrational band patterns of the cryogenically cooled, D2-tagged bn ions obtained using isomer-selective, two-color IR-IR photobleaching and analyzing them with predicted (DFT) harmonic spectra for the candidate structures. Both oxazolone and macrocyclic isomers are formed by b4, whereas only oxazolone species are created for b2 and b3 and the macrocycle is created for b5. As such, n = 4 corresponds to the minimum size where both Oxa and MC forms are present.
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Affiliation(s)
- Ahmed Mohamed
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Abhijit Rana
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Evan Perez
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- The University of Utah, 315 S. 1400 E. Rm 2020, Henry Eyring Bldg, Salt Lake City, Utah 84112, United States
| | - Franziska Dahlmann
- Institut for Ion Physics and Applied Physics, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Allison Fry
- Center of Excellence in Mass Spectrometry, Center for Metal Ions in Biological and Chemical Systems, Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Fabian S Menges
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Michael van Stipdonk
- Center of Excellence in Mass Spectrometry, Center for Metal Ions in Biological and Chemical Systems, Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Svenja Jäger
- Chair of Physical Chemistry II, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Mark A Boyer
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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Finazzi L, Martens J, Berden G, Oomens J. Probing radical versus proton migration in the aniline cation with IRMPD spectroscopy. Mol Phys 2023. [DOI: 10.1080/00268976.2023.2192307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Mookherjee A, Armentrout PB. Thermodynamics and Reaction Mechanisms for Decomposition of a Simple Protonated Tripeptide, H +GGA: From H +GGG to H +GAG to H +GGA. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:355-368. [PMID: 34981933 DOI: 10.1021/jasms.1c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We present a thorough characterization of fragmentations observed in threshold collision-induced dissociation (TCID) experiments of protonated glycylglycylalanine (H+GGA) with Xe using a guided ion beam tandem mass spectrometer. Kinetic energy dependent cross sections for nine ionic products were obtained and analyzed to provide 0 K barriers for the five primary products, [b2]+, [y1 + 2H]+, [b3]+, [y2 + 2H]+, and [a1]+; and four secondary products, [a2]+, [a3]+, high-energy [y1 + 2H]+, and CH3CHNH2+, after accounting for multiple ion-molecule collisions, the internal energy of reactant ions, unimolecular decay rates, competition between channels, and sequential dissociations. Relaxed potential energy surface scans performed at the B3LYP-GD3BJ/6-311+G(d,p) level of theory are used to identify transition states (TSs) and intermediates of the five primary and three secondary products (with the mechanism of the other secondary product previously established). Geometry optimizations and single point energy calculations of reactants, products, intermediates, and TSs were performed at several levels of theory. These theoretical energies are compared with experimental threshold energies and found to give reasonable agreement, with B3LYP-GD3BJ and M06-2X levels of theory performing slightly better than MP2 and better than B3LYP. The results obtained here are compared with previous results for decomposition of H+GGG and H+GAG to probe the effect of changing the amino acid sequence. Methylation in H+GGA has a significant effect on the competition between the primary sequence products, [b2]+ and [y1 + 2H]+, suppressing the [b2]+ cross section by raising its threshold energy, while enhancing that of [y1 + 2H]+ by lowering its threshold energy.
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Affiliation(s)
- Abhigya Mookherjee
- Department of Chemistry, University of Utah, 315 S. 1400 E., Room 2020, Salt Lake City, Utah 84112, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E., Room 2020, Salt Lake City, Utah 84112, United States
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5
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Atik A, Arslanoglu A, Yalcin T. Gas-phase fragmentation reactions of a 7 ions containing a glutamine residue. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4776. [PMID: 34268823 DOI: 10.1002/jms.4776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
The gas-phase fragmentation reactions of the a7 ions derived from glutamine (Q) containing model heptapeptides have been studied in detail with low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). Specifically, the positional effect of the Q residue has been investigated on the fragmentation reactions of a7 ions. The study involves two sets of permuted isomers of the Q containing model heptapeptides. The first set contains the QAAAAAA sequence, and the second set involves of QYAGFLV sequence, where the position of the Q residue is changed from N- to C-terminal gradually for both peptide series. An intense loss of ammonia from the a7 ions followed by internal amino acid eliminations strongly supports forming the imine-amides structure via cyclization/rearrangement reaction for all studied a7 ions. This is in agreement with the pioneering study reported by Bythell et al. (2010, 10.1021/ja101556g). A novel rearrangement reaction is detected upon fragmentation of imine-amide structure, which yields a protonated C-terminal amidated hexapeptide excluding the Q residue. A possible fragmentation mechanism was proposed to form the protonated C-terminal amidated hexapeptide, assisted via nucleophilic attack of the side chain amide nitrogen of the Q residue on its N-protonated imine carbon atom of the rearranged imine-amide structure. HIGHLIGHTS: The gas-phase fragmentation reactions of a7 ions obtained from protonated model peptides containing glutamine residue were studied by ESI-MS/MS. A rearranged imine-amide structure is the predominant even for a7 ions. Novel rearrangement reaction is observed which forms a protonated C-terminal amidated hexapeptide excluding Q residue upon fragmentation of the imine-amide structure.
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Affiliation(s)
- Ahmet Atik
- Department of Natural Sciences, Faculty of Engineering, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Biotechnology Group, Turgut Pharmaceuticals, Istanbul, Turkey
| | - Alper Arslanoglu
- Departmen of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, Izmir, Turkey
| | - Talat Yalcin
- Department of Chemistry, Faculty of Science, Izmir Institute of Technology, Izmir, Turkey
- Integrated Research Centers, National Mass Spectrometry Application and Research Center, Izmir, Turkey
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6
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Lau JKC, Esuon F, Berden G, Oomens J, Hopkinson AC, Ryzhov V, Siu KWM. Generation, Characterization, and Dissociation of Radical Cations Derived from Prolyl-glycyl-glycine. J Phys Chem B 2021; 125:6121-6129. [PMID: 34097420 DOI: 10.1021/acs.jpcb.1c01732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Radical cations of an aliphatic tripeptide prolyl-glycyl-glycine (PGG•+) and its sequence ions [a3 + H]•+ and [b2 - H]•+ have been generated by collision-induced dissociation of the [Cu(Phen)(PGG)]•2+ complex, where Phen = 1,10-phenanthroline. Infrared multiple photon dissociation spectroscopy, ion-molecule reaction experiments, and theoretical calculations have been used to investigate the structures of these ions. The unpaired electron in these three radical cations is located at different α-carbons. The PGG•+ radical cation has a captodative structure with the radical at the α-carbon of the proline residue and the proton on the oxygen of the first amide group. This structure is at the global minimum on the potential energy surface (PES). By contrast, the [a3 + H]•+ and [b2 - H]•+ ions are not the lowest-energy structures on their respective PESs, and their radicals are formally located at the C-terminal and second α-carbons, respectively. Density functional theory calculations on the structures of the ternary copper(II) complex ion suggest that the charge-solvated isomer of the metal complex is the precursor ion that dissociates to give the PGG•+ radical cation. The isomer of the complex in which PGG is bound as a zwitterion dissociates to give the [a3 + H]•+ and [b2 - H]•+ ions.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | - Francis Esuon
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, the Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, the Netherlands
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
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7
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Guan S, Bythell BJ. Size Dependent Fragmentation Chemistry of Short Doubly Protonated Tryptic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1020-1032. [PMID: 33779179 DOI: 10.1021/jasms.1c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tandem mass spectrometry of electrospray ionized multiply charged peptide ions is commonly used to identify the sequence of peptide(s) and infer the identity of source protein(s). Doubly protonated peptide ions are consistently the most efficiently sequenced ions following collision-induced dissociation of peptides generated by tryptic digestion. While the broad characteristics of longer (N ≥ 8 residue) doubly protonated peptides have been investigated, there is comparatively little data on shorter systems where charge repulsion should exhibit the greatest influence on the dissociation chemistry. To address this gap and further understand the chemistry underlying collisional-dissociation of doubly charged tryptic peptides, two series of analytes ([GxR+2H]2+ and [AxR+2H]2+, x = 2-5) were investigated experimentally and with theory. We find distinct differences in the preference of bond cleavage sites for these peptides as a function of size and to a lesser extent composition. Density functional calculations at two levels of theory predict that the threshold relative energies required for bond cleavages at the same site for peptides of different size are quite similar (for example, b2-yN-2). In isolation, this finding is inconsistent with experiment. However, the predicted extent of entropy change of these reactions is size dependent. Subsequent RRKM rate constant calculations provide a far clearer picture of the kinetics of the competing bond cleavage reactions enabling rationalization of experimental findings. The M06-2X data were substantially more consistent with experiment than were the B3LYP data.
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Affiliation(s)
- Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
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8
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Oomens J, Kempkes LJM, Geurts TPJ, van Dijk L, Martens J, Berden G, Armentrout PB. Water Loss from Protonated XxxSer and XxxThr Dipeptides Gives Oxazoline-Not Oxazolone-Product Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2111-2123. [PMID: 32876444 PMCID: PMC7552115 DOI: 10.1021/jasms.0c00239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Neutral loss of water and ammonia are often significant fragmentation channels upon collisional activation of protonated peptides. Here, we deploy infrared ion spectroscopy to investigate the dehydration reactions of protonated AlaSer, AlaThr, GlySer, GlyThr, PheSer, PheThr, ProSer, ProThr, AsnSer, and AsnThr, focusing on the question of the structure of the resulting [M + H - H2O]+ fragment ion and the site from which H2O is expelled. In all cases, the second residue of the selected peptides contains a hydroxyl moiety, so that H2O loss can potentially occur from this side-chain, as an alternative to loss from the C-terminal free acid of the dipeptide. Infrared action spectra of the product ions along with quantum-chemical calculations unambiguously show that dehydration consistently produces fragment ions containing an oxazoline moiety. This contrasts with the common oxazolone structure that would result from dehydration at the C-terminus analogous to the common b/y dissociation forming regular b2-type sequence ions. The oxazoline product structure suggests a reaction mechanism involving water loss from the Ser/Thr side-chain with concomitant nucleophilic attack of the amide carbonyl oxygen at its β-carbon, forming an oxazoline ring. However, an extensive quantum-chemical investigation comparing the potential energy surfaces for three entirely different dehydration reaction pathways indicates that it is actually the backbone amide oxygen atom that leaves as the water molecule.
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Affiliation(s)
- Jos Oomens
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
- Van’t Hoff Institute for Molecular Sciences,
University of Amsterdam, Science Park 904, 1098 XH Amsterdam,
The Netherlands
| | - Lisanne J. M. Kempkes
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Thijs P. J. Geurts
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Luuk van Dijk
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of
Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112,
United States
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9
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Cautereels J, Giribaldi J, Enjalbal C, Blockhuys F. Quantum chemical mass spectrometry: Ab initio study of b 2 -ion formation mechanisms for the singly protonated Gln-His-Ser tripeptide. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8778. [PMID: 32144813 DOI: 10.1002/rcm.8778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Both amide bond protonation triggering peptide fragmentations and the controversial b2 -ion structures have been subjects of intense research. The involvement of histidine (H), with its imidazole side chain that induces specific dissociation patterns involving inter-side-chain (ISC) interactions, in b2 -ion formation was investigated, focusing on the QHS model tripeptide. METHODS To identify the effect of histidine on fragmentations issued from ISC interactions, QHS was selected for a comprehensive analysis of the pathways leading to the three possible b2 -ion structures, using quantum chemical calculations performed at the DFT/B3LYP/6-311+G* level of theory. Electrospray ionization ion trap mass spectrometry allowed the recording of MS2 and MS3 tandem mass spectra, whereas the Quantum Chemical Mass Spectrometry for Materials Science (QCMS2 ) method was used to predict fragmentation patterns. RESULTS Whereas it is very difficult to differentiate among protonated oxazolone, diketopiperazine, or lactam b2 -ions using MS2 and MS3 mass spectra, the calculations indicated that the QH b2 -ion (detected at m/z 266) is probably a mixture of the lactam and oxazolone structures formed after amide nitrogen protonation, making the formation of diketopiperazine less likely as it requires an additional step for its formation. CONCLUSIONS In contrast to glycine-histidine-containing b2 -ions, known to be issued from the backbone-imidazole cyclization, we found that interactions between the side chains were not obvious to perceive, neither from a thermodynamics nor from a fragmentation perspective, emphasizing the importance of the whole sequence on the dissociation behavior usually demonstrated from simple glycine-containing tripeptides.
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Affiliation(s)
- Julie Cautereels
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | | | | | - Frank Blockhuys
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
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10
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Martens J, van Outersterp RE, Vreeken RJ, Cuyckens F, Coene KLM, Engelke UF, Kluijtmans LAJ, Wevers RA, Buydens LMC, Redlich B, Berden G, Oomens J. Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective. Anal Chim Acta 2019; 1093:1-15. [PMID: 31735202 DOI: 10.1016/j.aca.2019.10.043] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 01/21/2023]
Abstract
Combining the individual analytical strengths of mass spectrometry and infrared spectroscopy, infrared ion spectroscopy is increasingly recognized as a powerful tool for small-molecule identification in a wide range of analytical applications. Mass spectrometry is itself a leading analytical technique for small-molecule identification on the merit of its outstanding sensitivity, selectivity and versatility. The foremost shortcoming of the technique, however, is its limited ability to directly probe molecular structure, especially when contrasted against spectroscopic techniques. In infrared ion spectroscopy, infrared vibrational spectra are recorded for mass-isolated ions and provide a signature that can be matched to reference spectra, either measured from standards or predicted using quantum-chemical calculations. Here we present an overview of the potential for this technique to develop into a versatile analytical method for identifying molecular structures in mass spectrometry-based analytical workflows. In this tutorial perspective, we introduce the reader to the technique of infrared ion spectroscopy and highlight a selection of recent experimental advances and applications in current analytical challenges, in particular in the field of untargeted metabolomics. We report on the coupling of infrared ion spectroscopy with liquid chromatography and present experiments that serve as proof-of-principle examples of strategies to address outstanding challenges.
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Affiliation(s)
- Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands.
| | - Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Rob J Vreeken
- Drug Metabolism & Pharmacokinetics, Janssen R&D, Beerse, Belgium
| | - Filip Cuyckens
- Drug Metabolism & Pharmacokinetics, Janssen R&D, Beerse, Belgium
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Udo F Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lutgarde M C Buydens
- Radboud University, Institute for Molecules and Materials, Chemometrics, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Britta Redlich
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands; van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098XH, Amsterdam, Science Park 908, the Netherlands.
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11
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Smith ZM, Wang X, Scheerer JR, Martens J, Berden G, Oomens J, Steinmetz V, Somogyi A, Wysocki V, Poutsma JC. Spectroscopic Evidence for Lactam Formation in Terminal Ornithine b 2+ and b 3+ Fragment Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1565-1577. [PMID: 31183839 PMCID: PMC6697629 DOI: 10.1007/s13361-019-02244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Infrared multiple photon dissociation action spectroscopy was performed on the AlaOrn b2+ and AlaAlaOrn b3+ fragment ions from ornithine-containing tetrapeptides. Infrared spectra were obtained in the fingerprint region (1000-2000 cm-1) using the infrared free electron lasers at the Centre Laser Infrarouge d'Orsay (CLIO) facility in Orsay, France, and the free electron lasers for infrared experiments (FELIX) facility in Nijmegen, the Netherlands. A novel terminal ornithine lactam AO+ b2+ structure was synthesized for experimental comparison and spectroscopy confirms that the b2+ fragment ion from AOAA forms a lactam structure. Comparison of experimental spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory shows that AO+ b2+ forms a terminal lactam protonated either on the lactam carbonyl oxygen or the N-terminal nitrogen atom. Several low-lying conformers of these isomers are likely populated following IRMPD dissociation. Similarly, a comparison of the experimental IRMPD spectrum with calculated spectra shows that AAO+ b3+-ions also adopt a lactam structure, again with multiple different protonation sites, during fragmentation. This study provides spectroscopic confirmation for the lactam cyclization proposed for the "ornithine effect" and represents an alternative bn+ structure to the oxazolone and diketopiperazine/macrocycle structures most often formed.
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Affiliation(s)
- Zachary M Smith
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Xiye Wang
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Jonathan R Scheerer
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Vincent Steinmetz
- Laboratorie de Chimie Physique, CNRS UMR 8000, Université Paris, 91405, Orsay, France
| | - Arpad Somogyi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210-1173, USA
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210-1173, USA
| | - John C Poutsma
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA.
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12
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Martens J, Berden G, Bentlage H, Coene KLM, Engelke UF, Wishart D, van Scherpenzeel M, Kluijtmans LAJ, Wevers RA, Oomens J. Unraveling the unknown areas of the human metabolome: the role of infrared ion spectroscopy. J Inherit Metab Dis 2018; 41:367-377. [PMID: 29556837 PMCID: PMC5959965 DOI: 10.1007/s10545-018-0161-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
The identification of molecular biomarkers is critical for diagnosing and treating patients and for establishing a fundamental understanding of the pathophysiology and underlying biochemistry of inborn errors of metabolism. Currently, liquid chromatography/high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy are the principle methods used for biomarker research and for structural elucidation of small molecules in patient body fluids. While both are powerful techniques, several limitations exist that often make the identification of unknown compounds challenging. Here, we describe how infrared ion spectroscopy has the potential to be a valuable orthogonal technique that provides highly-specific molecular structure information while maintaining ultra-high sensitivity. Here, we characterize and distinguish two well-known biomarkers of inborn errors of metabolism, glutaric acid for glutaric aciduria and ethylmalonic acid for short-chain acyl-CoA dehydrogenase deficiency, using infrared ion spectroscopy. In contrast to tandem mass spectra, in which ion fragments can hardly be predicted, we show that the prediction of an IR spectrum allows reference-free identification in the case that standard compounds are either commercially or synthetically unavailable. Finally, we illustrate how functional group information can be obtained from an IR spectrum for an unknown and how this is valuable information to, for example, narrow down a list of candidate structures resulting from a database query. Early diagnosis in inborn errors of metabolism is crucial for enabling treatment and depends on the identification of biomarkers specific for the disorder. Infrared ion spectroscopy has the potential to play a pivotal role in the identification of challenging biomarkers.
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Affiliation(s)
- Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands.
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Herman Bentlage
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Udo F Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - David Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Monique van Scherpenzeel
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands.
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands.
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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13
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Iacobucci C, Reale S, Aschi M, Oomens J, Berden G, De Angelis F. An Unprecedented Retro-Mumm Rearrangement Revealed by ESI-MS/MS, IRMPD Spectroscopy, and DFT Calculations. Chemistry 2018. [DOI: 10.1002/chem.201800347] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Claudio Iacobucci
- Current address: Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Strasse 4 06120 Halle (Saale) Germany
- Dipartimento di Scienze Fisiche e Chimiche; Università degli Studi dell'Aquila; Via Vetoio, Coppito 67100 L'Aquila Italy
| | - Samantha Reale
- Dipartimento di Scienze Fisiche e Chimiche; Università degli Studi dell'Aquila; Via Vetoio, Coppito 67100 L'Aquila Italy
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche; Università degli Studi dell'Aquila; Via Vetoio, Coppito 67100 L'Aquila Italy
| | - Jos Oomens
- Radboud University Nijmegen; Institute for Molecules and Materials, FELIX Laboratory; Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Giel Berden
- Radboud University Nijmegen; Institute for Molecules and Materials, FELIX Laboratory; Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Francesco De Angelis
- Dipartimento di Scienze Fisiche e Chimiche; Università degli Studi dell'Aquila; Via Vetoio, Coppito 67100 L'Aquila Italy
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14
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Poutsma JC, Martens J, Oomens J, Maitre P, Steinmetz V, Bernier M, Jia M, Wysocki V. Infrared Multiple-Photon Dissociation Action Spectroscopy of the b 2+ Ion from PPG: Evidence of Third Residue Affecting b 2+ Fragment Structure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1482-1488. [PMID: 28374317 PMCID: PMC5484043 DOI: 10.1007/s13361-017-1659-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 06/07/2023]
Abstract
Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b2+ fragment ion from the protonated PPG tripeptide. Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. This result is in contrast with a recent study of the IRMPD action spectrum of the PP b2+ fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. Int. J. Mass Spectrom. 2015, 377, 179). The diketopiperazine b2+ ion is thermodynamically more stable than the oxazolone but normally requires a trans/cis peptide bond isomerization in the dissociating peptide. Martens et al. showed through IRMPD action spectroscopy that the PPP precursor ion was in a conformation in which the first peptide bond is already in the cis conformation and thus it was energetically favorable to form the thermodynamically-favored diketopiperazine b2+ ion. In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPG precursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation. Graphical Abstract ᅟ.
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Affiliation(s)
- John C Poutsma
- Department of Chemistry, College of William and Mary, Williamsburg, VA, 23187, USA.
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525ED, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525ED, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 908, 1098XH, Amsterdam, The Netherlands
| | - Phillipe Maitre
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris Sud, Université Paris Saclay, CNRS, Orsay, France
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris Sud, Université Paris Saclay, CNRS, Orsay, France
| | - Matthew Bernier
- Department of Chemistry, Ohio State University, Columbus, OH, 43210, USA
| | - Mengxuan Jia
- Department of Chemistry, Ohio State University, Columbus, OH, 43210, USA
| | - Vicki Wysocki
- Department of Chemistry, Ohio State University, Columbus, OH, 43210, USA.
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15
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Koirala D, Mistry S, Wenthold PG. Participation of C-H Protons in the Dissociation of a Proton Deficient Dipeptide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1313-1323. [PMID: 28429299 DOI: 10.1007/s13361-017-1662-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
The dissociation of anionic dipeptides Phe*Gly and GlyPhe*, where Phe* refers to sulfonated phenyl alanine, has been investigated by using ion trap mass spectrometry. The dipeptides undergo collision-induced dissociation (CID) to give the same products, indicating that they rearrange to a common structure before dissociation. The rearrangement does not occur with the dipeptide methyl esters. The structures of the b2 ions were investigated to determine the effect that having a remote, anionic site has on product formation. Comparison with the CID spectra for authentic structures shows that the b2 ion obtained from GlyPhe* has predominantly a diketopiperazine structure. The CID spectra for the Phe*Gly b2 ion and the authentic oxazolone are similar, but differences in intensity suggest a two-component mixture. Isotopic labeling studies are consistent with the formation of two products, with one resulting from loss of a non-mobile proton on the Gly α-carbon. The results are attributed to the formation of an oxazole and oxazolone enol product. Electronic structure calculations predict that the enol structure of the Phe*Gly b2 ion is lower in energy than the keto version due to intramolecular hydrogen bonding with the sulfonate group. Graphical Abstract ᅟ.
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Affiliation(s)
- Damodar Koirala
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA
| | - Sabyasachy Mistry
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA
| | - Paul G Wenthold
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA.
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16
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Mookherjee A, Van Stipdonk MJ, Armentrout PB. Thermodynamics and Reaction Mechanisms of Decomposition of the Simplest Protonated Tripeptide, Triglycine: A Guided Ion Beam and Computational Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:739-757. [PMID: 28197927 DOI: 10.1007/s13361-016-1590-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 06/06/2023]
Abstract
We present a thorough characterization of fragmentations observed in threshold collision-induced dissociation (TCID) experiments of protonated triglycine (H+GGG) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Kinetic energy-dependent cross-sections for 10 ionic products are observed and analyzed to provide 0 K barriers for six primary products: [b2]+, [y1 + 2H]+, [b3]+, CO loss, [y2 + 2H]+, and [a1]+; three secondary products: [a2]+, [a3]+, and [y2 + 2H - CO]+; and two tertiary products: high energy [y1 + 2H]+ and [a2 - CO]+ after accounting for multiple ion-molecule collisions, internal energy of reactant ions, unimolecular decay rates, competition between channels, and sequential dissociations. Relaxed potential energy surface scans performed at the B3LYP-D3/6-311+G(d,p) level of theory are used to identify transition states (TSs) and intermediates of the six primary and one secondary products. Geometry optimizations and single point energy calculations were performed at several levels of theory. These theoretical energies are compared with experimental energies and are found to give reasonably good agreement, in particular for the M06-2X level of theory. This good agreement between experiment and theory validates the reaction mechanisms explored computationally here and elsewhere and allows identification of the product structures formed at threshold energies. The present work presents the first measurement of absolute experimental threshold energies of important sequence ions and non-sequence ions: [y1 + 2H]+, [b3]+, CO loss, [a1]+, and [a3]+, and refines those for [b2]+ and [y2 + 2H]+ previously measured. Graphical Abstract ᅟ.
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Affiliation(s)
- Abhigya Mookherjee
- Department of Chemistry, University of Utah, 315 S.1400 E. Rm 2020, Salt Lake City, UT, 84112, USA
| | - Michael J Van Stipdonk
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave., Pittsburg, PA, 15282, USA
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 S.1400 E. Rm 2020, Salt Lake City, UT, 84112, USA.
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17
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Lau JKC, Zhao J, Williams D, Wu BHB, Wang Y, Mädler S, Saminathan IS, Siu KWM, Hopkinson AC. Radical-induced dissociation leading to the loss of CO2 from the oxazolone ring of [b5- H]˙(+) ions. Phys Chem Chem Phys 2016; 18:18119-27. [PMID: 27327880 DOI: 10.1039/c6cp01974a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Macrocyclization is commonly observed in large bn(+) (n≥ 4) ions and as a consequence can lead to incorrect protein identification due to sequence scrambling. In this work, the analogous [b5- H]˙(+) radical cations derived from aliphatic hexapeptides (GA5˙(+)) also showed evidence of macrocyclization under CID conditions. However, the major fragmentation for [b5- H]˙(+) ions is the loss of CO2 and not CO loss, which is commonly observed in closed-shell bn(+) ions. Isotopic labeling using CD3 and (18)O revealed that more than one common structure underwent dissociations. Theoretical studies found that the loss of CO2 is radical-driven and is facilitated by the radical being located at the Cα atom immediately adjacent to the oxazolone ring. Comparable energy barriers against macrocyclization, hydrogen-atom transfer, and fragmentations are found by DFT calculations and the results are consistent with the experimental observations that a variety of dissociation products are observed in the CID spectra.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
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18
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Martens J, Grzetic J, Berden G, Oomens J. Structural identification of electron transfer dissociation products in mass spectrometry using infrared ion spectroscopy. Nat Commun 2016; 7:11754. [PMID: 27277826 PMCID: PMC4906228 DOI: 10.1038/ncomms11754] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/27/2016] [Indexed: 12/04/2022] Open
Abstract
Tandem mass spectrometry occupies a principle place among modern analytical methods and drives many developments in the ‘omics' sciences. Electron attachment induced dissociation methods, as alternatives for collision-induced dissociation have profoundly influenced the field of proteomics, enabling among others the top-down sequencing of entire proteins and the analysis of post-translational modifications. The technique, however, produces more complex mass spectra and its radical-driven reaction mechanisms remain incompletely understood. Here we demonstrate the facile structural characterization of electron transfer dissociation generated peptide fragments by infrared ion spectroscopy using the tunable free-electron laser FELIX, aiding the elucidation of the underlying dissociation mechanisms. We apply this method to verify and revise previously proposed product ion structures for an often studied model tryptic peptide, [AlaAlaHisAlaArg+2H]2+. Comparing experiment with theory reveals that structures that would be assigned using only theoretical thermodynamic considerations often do not correspond to the experimentally sampled species. Mass spectrometry is a leading method used for sequencing peptides and proteins by fragmentation followed by analysis of the sequence fragments. Here, the authors use infrared spectroscopy to characterize the structures of peptide fragments formed during electron transfer dissociation.
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Affiliation(s)
- Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Josipa Grzetic
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands.,Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 908, 1098XH Amsterdam, The Netherlands
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19
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Nelson CR, Abutokaikah MT, Harrison AG, Bythell BJ. Proton Mobility in b₂ Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:487-497. [PMID: 26602904 DOI: 10.1007/s13361-015-1298-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/13/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting.
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Affiliation(s)
- Carissa R Nelson
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA.
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20
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Plaviak A, Osburn S, Patterson K, van Stipdonk MJ. Even-electron [M-H](+) ions generated by loss of AgH from argentinated peptides with N-terminal imine groups. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:69-80. [PMID: 26661972 DOI: 10.1002/rcm.7415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/24/2015] [Accepted: 10/04/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Experiments were performed to probe the creation of apparent even-electron, [M-H](+) ions by CID of Ag-cationized peptides with N-terminal imine groups (Schiff bases). METHODS Imine-modified peptides were prepared using condensation reactions with aldehydes. Ag(+) -cationized precursors were generated by electrospray ionization (ESI). Tandem mass spectrometry (MS(n) ) and collision-induced dissociation (CID) were performed using a linear ion trap mass spectrometer. RESULTS Loss of AgH from peptide [M + Ag](+) ions, at the MS/MS stage, creates closed-shell [M-H](+) ions from imine-modified peptides. Isotope labeling unambiguously identifies the imine C-H group as the source of H eliminated in AgH. Subsequent CID of the [M-H](+) ions generated sequence ions that are analogous to those produced from [M + H](+) ions of the imine-modified peptides. CONCLUSIONS Experiments show (a) formation of novel even-electron peptide cations by CID and (b) the extent to which sequence ions (conventional b, a and y ions) are generated from peptides with fixed charge site and thus lacking a conventional mobile proton.
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Affiliation(s)
- Alexandra Plaviak
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Sandra Osburn
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Khiry Patterson
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Michael J van Stipdonk
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
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21
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Masson A, Williams ER, Rizzo TR. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine. J Chem Phys 2015; 143:104313. [DOI: 10.1063/1.4930196] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Antoine Masson
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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22
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Aseev O, Perez MAS, Rothlisberger U, Rizzo TR. Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling. J Phys Chem Lett 2015; 6:2524-2529. [PMID: 26266729 DOI: 10.1021/acs.jpclett.5b01088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Collision-induced dissociation (CID) is a key technique used in mass spectrometry-based peptide sequencing. Collisionally activated peptides undergo statistical dissociation, forming a series of backbone fragment ions that reflect their amino acid (AA) sequence. Some of these fragments may experience a "head-to-tail" cyclization, which after proton migration, can lead to the cyclic structure opening in a different place than the initially formed bond. This process leads to AA sequence scrambling that may hinder sequencing of the initial peptide. Here we combine cryogenic ion spectroscopy and ab initio molecular dynamics simulations to isolate and characterize the precise structures of key intermediates in the scrambling process. The most stable peptide fragments show intriguing symmetric cyclic structures in which the proton is situated on a C2 symmetry axis and forms exceptionally short H-bonds (1.20 Å) with two backbone oxygens. Other nonsymmetric cyclic structures also exist, one of which is protonated on the amide nitrogen, where ring opening is likely to occur.
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Affiliation(s)
- Oleg Aseev
- †Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Marta A S Perez
- ‡Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCBC, Station 6, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- ‡Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCBC, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R Rizzo
- †Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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23
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Bythell BJ, Harrison AG. Formation of a(1) ions directly from oxazolone b(2) ions: an energy-resolved and computational study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:774-781. [PMID: 25810075 DOI: 10.1007/s13361-015-1080-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
It is well-known that oxazolone b2 ions fragment extensively by elimination of CO to form a2 ions, which often fragment further to form a1 ions. Less well-known is that some oxazolone b2 ions may fragment directly to form a1 ions. The present study uses energy-resolved collision-induced dissociation experiments to explore the occurrence of the direct b2→a1 fragmentation reaction. The experimental results show that the direct b2→a1 reaction is generally observed when Gly is the C-terminal residue of the oxazolone. When the C-terminal residue is more complex, it is able to provide increased stability of the a2 product in the b2→a2 fragmentation pathway. Our computational studies of the relative critical reaction energies for the b2→a2 reaction compared with those for the b2→a1 reaction provide support that the critical reaction energies are similar for the two pathways when the C-terminal residue of the oxazolone is Gly. By contrast, when the nitrogen of the oxazolone ring in the b2 ion does not bear a hydrogen, as in the Ala-Sar and Tyr-Sar (Sar = N-methylglycine) oxazolone b2 ions, a1 ions are not formed but rather neutral imine elimination from the N-terminus of the b2 ion becomes a dominant fragmentation reaction. The M06-2X/6-31+G(d,p) density functional theory calculations are in general agreement with the experimental data for both types of reaction. In contrast, the B3LYP/6-31+G(d,p) model systematically underestimates the barriers of these SN2-like b2→a1 reaction. The difference between the two methods of barrier calculation are highly significant (P < 0.001) for the b2→a1 reaction, but only marginally significant (P = 0.05) for the b2→a2 reaction. The computations provide further evidence of the limitations of the B3LYP functional when describing SN2-like reactions.
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Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, 63131, USA,
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24
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Yoon HJ, Seo J, Shin SK. Multi-functional MBIT for peptide tandem mass spectrometry. MASS SPECTROMETRY REVIEWS 2015; 34:209-218. [PMID: 24872020 DOI: 10.1002/mas.21435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 11/20/2013] [Accepted: 03/26/2014] [Indexed: 06/03/2023]
Abstract
Isobaric tags have been widely used for the identification and quantification of proteins in mass spectrometry-based proteomics. The mass-balanced, (1) H/(2) H isotope-coded dipeptide tag (MBIT) is a multifunctional isobaric tag based on N-acetyl-Ala-Ala dipeptide containing an amine-reactive linker that conjugates the tag to the primary amines of proteolytic peptides. MBITs provide a pair of isotope-coded quantitation signals separated by 3 Da, which enables 2-plex quantification and identification of proteins in the 15-250 fmol range. Various MBITs diversified at the N-acetyl group or at the side chain of the first alanine provide a pair of bs ions as low-mass quantitation signals in a distinct mass window. Thus, a combination of different MBITs allows multiplex quantification of proteins in a single liquid chromatography-mass spectrometry experiment. Unlike other isobaric tags, MBITs also offer a pair of ys ions as high-mass quantitation signals in a noise-free region, facilitating protein quantification in quadrupole ion trap mass spectrometers. Uniquely, bS ions, forming N-protonated oxazolone, undergo unimolecular dissociation and generate the secondary low-mass quantitation signals, aS ions. The yield of aS ions derived from bS ions can be used to measure the temperature of bS ions, which enables a reproducible acquisition of the peptide tandem mass spectra. Thus, MBITs enable multiplexed quantitation of proteins and the concurrent measurement of ion temperature using bS and aS signal ions as well as the isobaric protein quantitation in resonance-type ion trap using yS (complement of bS ) signal ions. This review provides an overview of MBITs with a focus on the multi-functionality that has been successfully demonstrated in the peptide tandem mass spectrometry.
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Affiliation(s)
- Hye-Joo Yoon
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
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Wang H, Wang B, Wei Z, Zhang H, Guo X. Structure and further fragmentation of significant [a3 + Na - H]+ ions from sodium-cationized peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:212-219. [PMID: 25601695 DOI: 10.1002/jms.3520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 09/21/2014] [Accepted: 10/02/2014] [Indexed: 06/04/2023]
Abstract
A good understanding of gas-phase fragmentation chemistry of peptides is important for accurate protein identification. Additional product ions obtained by sodiated peptides can provide useful sequence information supplementary to protonated peptides and improve protein identification. In this work, we first demonstrate that the sodiated a3 ions are abundant in the tandem mass spectra of sodium-cationized peptides although observations of a3 ions have rarely been reported in protonated peptides. Quantum chemical calculations combined with tandem mass spectrometry are used to investigate this phenomenon by using a model tetrapeptide GGAG. Our results reveal that the most stable [a3 + Na - H](+) ion is present as a bidentate linear structure in which the sodium cation coordinates to the two backbone carbonyl oxygen atoms. Due to structural inflexibility, further fragmentation of the [a3 + Na - H](+) ion needs to overcome several relatively high energetic barriers to form [b2 + Na - H](+) ion with a diketopiperazine structure. As a result, low abundance of [b2 + Na - H](+) ion is detected at relatively high collision energy. In addition, our computational data also indicate that the common oxazolone pathway to generate [b2 + Na - H](+) from the [a3 + Na - H](+) ion is unlikely. The present work provides a mechanistic insight into how a sodium ion affects the fragmentation behaviors of peptides.
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Affiliation(s)
- Huixin Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
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Liu P, Cooks RG, Chen H. Nuclear Magnetic Resonance Structure Elucidation of Peptideb2Ions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Liu P, Cooks RG, Chen H. Nuclear magnetic resonance structure elucidation of peptide b2 ions. Angew Chem Int Ed Engl 2014; 54:1547-50. [PMID: 25504444 DOI: 10.1002/anie.201410250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Indexed: 11/06/2022]
Abstract
Tandem mass spectrometry (MS/MS) is powerful for chemical identification but it is still insufficient for explicit ion structure determination. A strategy is introduced to elucidate MS fragment ion structures using NMR spectroscopy for the first time. In our experiments, precursor ions are dissociated at atmospheric pressure and the resulting fragment ions are identified by mass spectrometry but collected outside the mass spectrometer, making the subsequent NMR measurements possible. This new strategy has been applied to determine the chemical structure of the characteristic b2 fragment ion, a subject of longstanding debate in MS-based proteomics.
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Affiliation(s)
- Pengyuan Liu
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry & Edison Biotechnology Institute, Ohio University, Athens, OH 45701 (USA)
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Atik AE, Hernandez O, Maître P, Yalcin T. Specific rearrangement reactions of acetylated lysine containing peptide bn (n = 4-7) ion series. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:1290-1297. [PMID: 25476947 DOI: 10.1002/jms.3462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/05/2014] [Accepted: 08/05/2014] [Indexed: 06/04/2023]
Abstract
Characterization of ε-N-acetylated lysine containing peptides, one of the most prominent post-translational modifications of proteins, is an important goal for tandem mass spectrometry experiments. A systematic study for the fragmentation reactions of b ions derived from ε-N-acetyllysine containing model octapeptides (KAc YAGFLVG and YAKAc GFLVG) has been examined in detail. Collision-induced dissociation (CID) mass spectra of bn (n = 4-7) fragments of ε-N-acetylated lysine containing peptides are compared with those of N-terminal acetylated and doubly acetylated (both ε-N and N-terminal) peptides, as well as acetyl-free peptides. Both direct and nondirect fragments are observed for acetyl-free and singly acetylated (ε-N or N-terminal) peptides. In the case of ε-N-acetylated lysine containing peptides, however, specific fragment ions (m/z 309, 456, 569 and 668) are observed in CID mass spectra of bn (n = 4-7) ions. The CID mass spectra of these four ions are shown to be identical to those of selected protonated C-terminal amidated peptides. On this basis, a new type of rearrangement chemistry is proposed to account for the formation of these fragment ions, which are specific for ε-N-acetylated lysine containing peptides. Consistent with the observation of nondirect fragments, it is proposed that the b ions undergo head-to-tail macrocyclization followed by ring opening. The proposed reaction pathway assumes that bn (n = 4-7) of ε-N-acetylated lysine containing peptides has a tendency to place the KAc residue at the C-terminal position after macrocyclization/reopening mechanism. Then, following the loss of CO, it is proposed that the marker ions are the result of the loss of an acetyllysine imine as a neutral fragment.
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Affiliation(s)
- A Emin Atik
- Department of Chemistry, Faculty of Science, Izmir Institute of Technology, 35430, Urla-Izmir, Turkey
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Harper B, Miladi M, Solouki T. Loss of internal backbone carbonyls: additional evidence for sequence-scrambling in collision-induced dissociation of y-type ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1716-1729. [PMID: 25070583 DOI: 10.1007/s13361-014-0955-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/14/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAHAA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MS(n)), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.
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Affiliation(s)
- Brett Harper
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA
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Féraud G, Dedonder-Lardeux C, Soorkia S, Jouvet C. Photo-fragmentation spectroscopy of benzylium and 1-phenylethyl cations. J Chem Phys 2014; 140:024302. [PMID: 24437872 DOI: 10.1063/1.4858409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The electronic spectra of cold benzylium (C6H5-CH2 (+)) and 1-phenylethyl (C6H5-CH-CH3 (+)) cations have been recorded via photofragment spectroscopy. Benzylium and 1-phenylethyl cations produced from electrosprayed benzylamine and phenylethylamine solutions, respectively, were stored in a cryogenically cooled quadrupole ion trap and photodissociated by an OPO laser, scanned in parts of the UV and visible regions (600-225 nm). The electronic states and active vibrational modes of the benzylium and 1-phenylethyl cations as well as those of their tropylium or methyl tropylium isomers have been calculated with ab initio methods for comparison with the spectra observed. Sharp vibrational progressions are observed in the visible region while the absorption features are much broader in the UV. The visible spectrum of the benzylium cation is similar to that obtained in an argon tagging experiment [V. Dryza, N. Chalyavi, J. A. Sanelli, and E. J. Bieske, J. Chem. Phys. 137, 204304 (2012)], with an additional splitting assigned to Fermi resonances. The visible spectrum of the 1-phenylethyl cation also shows vibrational progressions. For both cations, the second electronic transition is observed in the UV, around 33,000 cm(-1) (4.1 eV) and shows a broadened vibrational progression. In both cases the S2 optimized geometry is non-planar. The third electronic transition observed around 40,000 cm(-1) (5.0 eV) is even broader with no apparent vibrational structures, which is indicative of either a fast non-radiative process or a very large change in geometry between the excited and the ground states. The oscillator strengths calculated for tropylium and methyl tropylium are weak. Therefore, these isomeric structures are most likely not responsible for these absorption features. Finally, the fragmentation pattern changes in the second and third electronic states: C2H2 loss becomes predominant at higher excitation energies, for both cations.
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Affiliation(s)
- Géraldine Féraud
- Physique des Interactions Ioniques et Moleculaires, UMR CNRS 7345, Aix-Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
| | - Claude Dedonder-Lardeux
- Physique des Interactions Ioniques et Moleculaires, UMR CNRS 7345, Aix-Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
| | - Satchin Soorkia
- Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud 11, 91405 Orsay Cedex, France
| | - Christophe Jouvet
- Physique des Interactions Ioniques et Moleculaires, UMR CNRS 7345, Aix-Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
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31
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Holland MC, Berden G, Oomens J, Meijer AJHM, Schäfer M, Gilmour R. Infrared Multiphoton Dissociation Spectroscopic Analysis of Noncovalent Interactions in Organocatalysis. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402845] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Patrick AL, Stedwell CN, Polfer NC. Differentiating sulfopeptide and phosphopeptide ions via resonant infrared photodissociation. Anal Chem 2014; 86:5547-52. [PMID: 24823797 DOI: 10.1021/ac500992f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The post-translational modifications sulfation and phosphorylation pose special challenges to mass spectral analysis due to their isobaric nature and their lability in the gas phase, as both types of peptides dissociate through similar channels upon collisional activation. Here, we present resonant infrared photodissociation based on diagnostic sulfate and phosphate OH stretches, as a means to differentiate sulfated from phosphorylated peptides within the framework of a mass spectrometry platform. The approach is demonstrated for a number of tyrosine-containing peptides, ranging from dipeptides (YG, pYG, and sYG) over tripeptides (GYR, GpYR, and GsYR), to more biologically relevant enkephalin peptides (YGGFL, pYGGFL, and sYGGFL). In all cases, the diagnostic ranges for sulfate OH stretches are established as 3580-3600 cm(-1) and can thus be distinguished from other characteristic hydrogen stretches, such as carboxylic acid OH, alcohol OH, and phosphate OH stretches.
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Affiliation(s)
- Amanda L Patrick
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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Morrison LJ, Chamot-Rooke J, Wysocki VH. IR action spectroscopy shows competitive oxazolone and diketopiperazine formation in peptides depends on peptide length and identity of terminal residue in the departing fragment. Analyst 2014; 139:2137-43. [PMID: 24618890 PMCID: PMC6467643 DOI: 10.1039/c4an00064a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The interplay between the entropically and enthalpically favored products of peptide fragmentation is probed using a combined experimental and theoretical approach. These b2 ion products can take either an oxazolone or diketopiperazine structure. Cleavage after the second amide bond is often a favorable process because the products are small ring structures that are particularly stable. These structures are structurally characterized by action IRMPD spectroscopy and semi-quantified using gas-phase hydrogen-deuterium exchange. The formation of the oxazolone and diketopiperazine has been thought to be largely governed by the identity of the first two residues at the N-terminus of the peptide. We show here that the length of the precursor peptide and identity of the third residue play a significant role in the formation of the diketopiperazine structure in peptides containing an N-terminal asparagine residue. This is additionally the first instance showing an N-terminal residue with an amide side chain can promote formation of the diketopiperazine b2 ion structure.
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Affiliation(s)
- L J Morrison
- Department of Chemistry and Biochemistry, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, USA.
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Harrison AG. Effect of the sarcosine residue on sequence scrambling in peptide b(5) ions. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:161-167. [PMID: 24464544 DOI: 10.1002/jms.3323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/24/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
The effect of N-methylation on sequence scrambling in the fragmentation of b5 ions has been investigated by studying a variety of peptides containing sarcosine (N-methylglycine). The product ion mass spectra for the b5 ions derived from Sar-A-A-A-Y-A and Sar-A-A-Y-A-A show only minor signals for non-direct sequence ions the major fragmentation reactions occurring from the unrearranged structures. This is in contrast to the b5 ions where the Sar residue is replaced by Ala and sequence scrambling occurs. The b5 ion derived from Y-Sar-A-A-A-A shows a product ion mass spectrum essentially identical to the spectrum of the b5 ion derived from Sar-A-A-A-Y-A, indicating that in the former case macrocyclization has occurred but the macrocyclic form shows a strong preference to reopen to put the Sar residue in the N-terminal position. Similar results were obtained in the comparison of b5 ions derived from A-Sar-A-A-Y-A and Sar-A-A-Y-A-A. The product ion mass spectra of the MH(+) ions of Y-Sar-A-A-A-A and A-Sar-A-A-Y-A show substantial signals for non-direct sequence ions indicating that fragmentation of the MH(+) ions channels extensively through the respective b5 ions and further fragmentation of these species.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, Canada
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Zhao J, Lau JKC, Grzetic J, Verkerk UH, Oomens J, Siu KWM, Hopkinson AC. Structures of a(n)* ions derived from protonated pentaglycine and pentaalanine: results from IRMPD spectroscopy and DFT calculations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1957-1968. [PMID: 24026976 DOI: 10.1007/s13361-013-0728-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 06/02/2023]
Abstract
Infrared multiple-photon dissociation (IRMPD) spectroscopy and DFT calculations have been used to probe the most stable structures of a3(*) and a4(*) ions derived from both protonated pentaglycine (denoted G5) and pentaalanine (A5). The a3(*) and a4(*) ions derived from protonated A5 feature a CHR=N-CHR'- group at the N-terminus and an oxazolone ring at the C-terminus, as proposed previously [J. Am. Soc. Mass Spectrom. 19, 1788-1798 (2008)]. The isomeric a4(*) ion derived from A5 with a 3,5-dihydro-4H-imidazol-4-one ring structure was calculated to have a slightly better energy than the oxazolone, but the barrier to its formation is higher and there was no evidence of this ion in the IRMPD spectrum. By contrast, the a4(*) and [a4 - H2O](+) (denoted a4(0)) ions from G5 gave strikingly similar IRMPD spectra and both have the 3,5-dihydro-4H-imidazol-4-one ring structure similar to that recently reported for the [GGGG + H - H2O](+) ion [Int. J. Mass Spectrom. 316-318, 268-272 (2012)]. In the absence of a solvent molecule, the pathway to the oxazolone is calculated to be lower than those to thermodynamically more stable products, the a4(0) and the a4(*) with the 3,5-dihydro-4H-imidazol-4-one ring structure. Incorporation of one water molecule is sufficient to reduce the barrier to formation of the a4(0) of G5 to below that for formation of the oxazolone. On the equivalent potential energy surface for protonated A5 the barrier to formation of the a4(0) ion is 12.3 kcal mol(-1) higher than that for oxazolone formation and the a4(0) ion is not observed experimentally.
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Affiliation(s)
- Junfang Zhao
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, ON, M3J 1P3, Canada
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Miladi M, Harper B, Solouki T. Evidence for sequence scrambling in collision-induced dissociation of y-type fragment ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1755-1766. [PMID: 23982935 DOI: 10.1007/s13361-013-0714-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 06/19/2013] [Accepted: 06/28/2013] [Indexed: 06/02/2023]
Abstract
Sequence scrambling from y-type fragment ions has not been previously reported. In a study designed to probe structural variations among b-type fragment ions, it was noted that y fragment ions might also yield sequence-scrambled ions. In this study, we examined the possibility and extent of sequence-scrambled fragment ion generation from collision-induced dissociation (CID) of y-type ions from four peptides (all containing basic residues near the C-terminus) including: AAAAHAA-NH2 (where "A" denotes carbon thirteen ((13)C1) isotope on the alanine carbonyl group), des-acetylated-α-melanocyte (SYSMEHFRWGKPV-NH2), angiotensin II antipeptide (EGVYVHPV), and glu-fibrinopeptide b (EGVNDNEEGFFSAR). We investigated fragmentation patterns of 32 y-type fragment ions, including y fragment ions with different charge states (+1 to +3) and sizes (3 to 12 amino acids). Sequence-scrambled fragment ions were observed from ~50 % (16 out of 32) of the studied y-type ions. However, observed sequence-scrambled ions had low relative intensities from ~0.1 % to a maximum of ~12 %. We present and discuss potential mechanisms for generation of sequence-scrambled fragment ions. To the best of our knowledge, results on y fragment dissociation presented here provide the first experimental evidence for generation of sequence-scrambled fragments from CID of y ions through intermediate cyclic "b-type" ions.
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Affiliation(s)
- Mahsan Miladi
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
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Harrison AG, Tasoglu C, Yalcin T. Non-direct sequence ions in the tandem mass spectrometry of protonated peptide amides--an energy-resolved study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1565-1572. [PMID: 23918462 DOI: 10.1007/s13361-013-0707-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/22/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
The fragmentation reactions of the MH(+) ions of Leu-enkephalin amide and a variety of heptapeptide amides have been studied in detail as a function of collision energy using a QqToF beam type mass spectrometer. The initial fragmentation of the protonated amides involves primarily formation of bn ions, including significant loss of NH3 from the MH(+) ions. Further fragmentation of these bn ions occurs following macrocyclization/ring opening leading in many cases to bn ions with permuted sequences and, thus, to formation of non-direct sequence ions. The importance of these non-direct sequence ions increases markedly with increasing collision energy, making peptide sequence determination difficult, if not impossible, at higher collision energies.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada,
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Zekavat B, Miladi M, Becker C, Munisamy SM, Solouki T. Combined use of post-ion mobility/collision-induced dissociation and chemometrics for b fragment ion analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1355-1365. [PMID: 23836377 DOI: 10.1007/s13361-013-0673-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/01/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
Although structural isomers may yield indistinguishable ion mobility (IM) arrival times and similar fragment ions in tandem mass spectrometry (MS), it is demonstrated that post-IM/collision-induced dissociation MS (post-IM/CID MS) combined with chemometrics can enable independent study of the IM-overlapped isomers. The new approach allowed us to investigate the propensity of selected b type fragment ions from AlaAlaAlaHisAlaAlaAla-NH2 (AAA(His)AAA) heptapeptide to form different isomers. Principle component analysis (PCA) of the unresolved post-IM/CID profiles indicated the presence of two different isomer types for b4(+), b5(+), and b6(+) and a single isomer type for b7(+) fragments of AAA(His)AAA. We employed a simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) to calculate the total IM profiles and CID mass spectra of b fragment isomers. The deconvoluted CID mass spectra showed discernible fragmentation patterns for the two isomers of b4(+), b5(+), and b6(+) fragments. Under our experimental conditions, calculated percentages of the "cyclic" isomers (at the 95% confidence level for n = 3) for b4(+), b5(+), and b6(+) were 61 (± 5)%, 36 (± 5)%, and 48 (± 2)%, respectively. Results from the SIMPLISMA deconvolution of b5(+) species resembled the CID MS patterns of fully resolved IM profiles for the two b5(+) isomers. The "cyclic" isomers for each of the two-component b fragment ions were less susceptible to ion fragmentation than their "linear" counterparts.
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Affiliation(s)
- Behrooz Zekavat
- Department of Chemistry and Biochemistry, Baylor University Sciences Building, Waco, TX 76798, USA
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Grzetic J, Oomens J. Spectroscopic identification of cyclic imide b2-ions from peptides containing Gln and Asn residues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1228-1241. [PMID: 23722727 DOI: 10.1007/s13361-013-0661-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/16/2013] [Accepted: 04/29/2013] [Indexed: 06/02/2023]
Abstract
In mass-spectrometry based peptide sequencing, formation of b- and y-type fragments by cleavage of the amide C-N bond constitutes the main dissociation pathway of protonated peptides under low-energy collision induced dissociation (CID). The structure of the b2 fragment ion from peptides containing glutamine (Gln) and asparagine (Asn) residues is investigated here by infrared ion spectroscopy using the free electron laser FELIX. The spectra are compared with theoretical spectra calculated using density functional theory for different possible isomeric structures as well as to experimental spectra of synthesized model systems. The spectra unambiguously show that the b2-ions do not possess the common oxazolone structure, nor do they possess the alternative diketopiperazine structure. Instead, cyclic imide structures are formed through nucleophilic attack by the amide nitrogen atom of the Gln and Asn side chains. The alternative pathway involving nucleophilic attack from the side-chain amide oxygen atom leading to cyclic isoimide structures, which had been suggested by several authors, can clearly be excluded based on the present IR spectra. This mechanism is perhaps surprising as the amide oxygen atom is considered to be the better nucleophile; however, computations show that the products formed via attack by the amide nitrogen are considerably lower in energy. Hence, b2-ions with Asn or Gln in the second position form structures with a five-membered succinimide or a six-membered glutarimide ring, respectively. b2-Ions formed from peptides with Asn in the first position are spectroscopically shown to possess the classical oxazolone structure.
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Affiliation(s)
- Josipa Grzetic
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, 6525ED, Nijmegen, The Netherlands
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Durand S, Rossa M, Hernandez O, Paizs B, Maître P. IR Spectroscopy of b4 Fragment Ions of Protonated Pentapeptides in the X–H (X = C, N, O) Region. J Phys Chem A 2013; 117:2508-16. [DOI: 10.1021/jp400634t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Sylvère Durand
- Laboratoire de Chimie Physique,
Université Paris Sud, UMR8000 CNRS, Faculté des Sciences,
Bât. 350, 91405 Orsay Cedex, France
| | - Maximiliano Rossa
- Laboratoire de Chimie Physique,
Université Paris Sud, UMR8000 CNRS, Faculté des Sciences,
Bât. 350, 91405 Orsay Cedex, France
| | - Oscar Hernandez
- Laboratoire de Chimie Physique,
Université Paris Sud, UMR8000 CNRS, Faculté des Sciences,
Bât. 350, 91405 Orsay Cedex, France
| | - Béla Paizs
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld
580, 69120 Heidelberg, Germany
- School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW,
U.K
| | - Philippe Maître
- Laboratoire de Chimie Physique,
Université Paris Sud, UMR8000 CNRS, Faculté des Sciences,
Bât. 350, 91405 Orsay Cedex, France
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Gucinski AC, Chamot-Rooke J, Steinmetz V, Somogyi Á, Wysocki VH. Influence of N-terminal residue composition on the structure of proline-containing b2+ ions. J Phys Chem A 2013; 117:1291-8. [PMID: 23312013 PMCID: PMC3641857 DOI: 10.1021/jp306759f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To probe the structural implications of the proline residue on its characteristic peptide fragmentation patterns, in particular its unusual cleavage at its C-terminus in formation of a b(2) ion in XxxProZzz sequences, the structures of a series of proline-containing b(2)(+) ions were studied by using action infrared multiphoton dissociation (IRMPD) spectroscopy and fragment ion hydrogen-deuterium exchange (HDX). Five different Xxx-Pro b(2)(+) ions were studied, with glycine, alanine, isoleucine, valine, or histidine in the N-terminal position. The residues selected feature different sizes, chain lengths, and gas phase basicities to explore whether the structure of the N-terminal residue influences the Xxx-Pro b(2)(+) ion structure. In proteins, the proline side chain-to-backbone attachment causes its peptide bonds to be in the cis conformation more than any other amino acid, although trans is still favored over cis. However, HP is the only b(2)(+) ion studied here that forms the diketopiperazine exclusively. The GP, AP, IP, and VP b(2)(+) ions formed from protonated tripeptide precursors predominantly featured oxazolone structures with small diketopiperazine contributions. In contrast to the b(2)(+) ions generated from tripeptides, synthetic cyclic dipeptides VP and HP were confirmed to have exclusive diketopiperazine structures.
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Affiliation(s)
- Ashley C Gucinski
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 East University Boulevard, P.O. Box 210041, Tucson, Arizona 85721-0041, USA.
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Novel selective and irreversible mosquito acetylcholinesterase inhibitors for controlling malaria and other mosquito-borne diseases. Sci Rep 2013; 3:1068. [PMID: 23323211 PMCID: PMC3545233 DOI: 10.1038/srep01068] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 12/19/2012] [Indexed: 12/03/2022] Open
Abstract
We reported previously that insect acetylcholinesterases (AChEs) could be selectively and irreversibly inhibited by methanethiosulfonates presumably through conjugation to an insect-specific cysteine in these enzymes. However, no direct proof for the conjugation has been published to date, and doubts remain about whether such cysteine-targeting inhibitors have desirable kinetic properties for insecticide use. Here we report mass spectrometric proof of the conjugation and new chemicals that irreversibly inhibited African malaria mosquito AChE with bimolecular inhibition rate constants (kinact/KI) of 3,604–458,597 M−1sec−1 but spared human AChE. In comparison, the insecticide paraoxon irreversibly inhibited mosquito and human AChEs with kinact/KI values of 1,915 and 1,507 M−1sec−1, respectively, under the same assay conditions. These results further support our hypothesis that the insect-specific AChE cysteine is a unique and unexplored target to develop new insecticides with reduced insecticide resistance and low toxicity to mammals, fish, and birds for the control of mosquito-borne diseases.
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Seo J, Suh MS, Yoon HJ, Shin SK. N-Acylated Dipeptide Tags Enable Precise Measurement of Ion Temperature in Peptide Fragmentation. J Phys Chem B 2012; 116:13982-90. [DOI: 10.1021/jp308697v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jongcheol Seo
- Bio-Nanotechnology Center, Department
of Chemistry, Pohang University of Science and Technology, San 31
Hyoja-dong Nam-gu, Pohang, 790-784, Korea
| | - Min-Soo Suh
- Bio-Nanotechnology Center, Department
of Chemistry, Pohang University of Science and Technology, San 31
Hyoja-dong Nam-gu, Pohang, 790-784, Korea
| | - Hye-Joo Yoon
- Bio-Nanotechnology Center, Department
of Chemistry, Pohang University of Science and Technology, San 31
Hyoja-dong Nam-gu, Pohang, 790-784, Korea
| | - Seung Koo Shin
- Bio-Nanotechnology Center, Department
of Chemistry, Pohang University of Science and Technology, San 31
Hyoja-dong Nam-gu, Pohang, 790-784, Korea
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Yang H, Good DM, van der Spoel D, Zubarev RA. Carbonyl charge solvation patterns may relate to fragmentation classes in collision-activated dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1319-1325. [PMID: 22689324 DOI: 10.1007/s13361-012-0418-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/12/2012] [Accepted: 05/13/2012] [Indexed: 06/01/2023]
Abstract
Here, we investigate the hypothesis that the origin of Class I fragmentation in tryptic peptide dications corresponding to the cleavage of the first two amino acids from the N-terminus is due to a dominant charge solvation pattern. Molecular dynamics simulations (MDS) of model A(n)R dications confirmed the existence of a persistent solvation of the protonated N-terminus on the second backbone carbonyl. Additionally, MDS predicted a new distinct fragmentation class corresponding to the loss of two amino acids from the C-terminus. This prediction was confirmed experimentally at very low excitation levels. The pattern produced by electron transfer dissociation of the same dications gave markedly decreased cleavage frequencies at the second peptide bond, which, within the non-local fragmentation mechanism, supports the preferential charge solvation on the second carbonyl. Taken together, these results confirm the role of a charge solvation pattern in the origin of fragmentation classes.
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Affiliation(s)
- Hongqian Yang
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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45
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Wassermann TN, Boyarkin OV, Paizs B, Rizzo TR. Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1029-1045. [PMID: 22460621 DOI: 10.1007/s13361-012-0368-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/17/2012] [Accepted: 02/23/2012] [Indexed: 05/31/2023]
Abstract
We have applied conformer-selective infrared-ultraviolet (IR-UV) double-resonance photofragment spectroscopy at low temperatures in an ion trap mass spectrometer for the spectroscopic characterization of peptide fragment ions. We investigate b- and a-type ions formed by collision-induced dissociation from protonated leucine-enkephalin. The vibrational analysis and assignment are supported by nitrogen-15 isotopic substitution of individual amino acid residues and assisted by density functional theory calculations. Under such conditions, b-type ions of different size are found to appear exclusively as linear oxazolone structures with protonation on the N-terminus, while a rearrangement reaction is confirmed for the a (4) ion in which the side chain of the C-terminal phenylalanine residue is transferred to the N-terminal side of the molecule. The vibrational spectra that we present here provide a particularly stringent test for theoretical approaches.
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Affiliation(s)
- Tobias N Wassermann
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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Tirado M, Polfer NC. Defying entropy: forming large head-to-tail macrocycles in the gas phase. Angew Chem Int Ed Engl 2012; 51:6436-8. [PMID: 22615257 DOI: 10.1002/anie.201202405] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Indexed: 11/08/2022]
Abstract
Spectral fingerprints: Collision-induced dissociation (CID) of protonated peptides in the gas phase results in linear fragment ions with a five-membered oxazolone ring on their C-terminal side. Infrared spectroscopy confirms that smaller fragments adopt oxazolone structures. Conversely, in mid-sized and larger fragments an isomerization to "head-to-tail" macrocycles is observed (see picture).
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Affiliation(s)
- Marcus Tirado
- Department of Chemistry, University of Florida, Buckman Drive, P.O. Box 117200, Gainesville, FL 32611, USA
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Tirado M, Polfer NC. Defying Entropy: Forming Large Head-to-Tail Macrocycles in the Gas Phase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Gucinski AC, Chamot-Rooke J, Nicol E, Somogyi Á, Wysocki VH. Structural influences on preferential oxazolone versus diketopiperazine b(2+) ion formation for histidine analogue-containing peptides. J Phys Chem A 2012; 116:4296-304. [PMID: 22448972 PMCID: PMC3523341 DOI: 10.1021/jp300262d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Studies of peptide fragment ion structures are important to aid in the accurate kinetic modeling and prediction of peptide fragmentation pathways for a given sequence. Peptide b(2)(+) ion structures have been of recent interest. While previously studied b(2)(+) ions that contain only aliphatic or simple aromatic residues are oxazolone structures, the HA b(2)(+) ion consists of both oxazolone and diketopiperazine structures. The structures of a series of histidine-analogue-containing Xxx-Ala b(2)(+) ions were studied by using action infrared multiphoton dissociation (IRMPD) spectroscopy, fragment ion hydrogen-deuterium exchange (HDX), and density functional theory (DFT) calculations to systematically probe the influence of different side chain structural elements on the resulting b(2)(+) ion structures formed. The b(2)(+) ions studied include His-Ala (HA), methylated histidine analogues, including π-methyl-HA and τ-methyl-HA, pyridylalanine (pa) analogues, including 2-(pa)A, 3-(pa)A, and 4-(pa)A, and linear analogues, including diaminobutanoic acid-Ala (DabA) and Lys-Ala (KA). The location and accessibility of the histidine π-nitrogen, or an amino nitrogen on an aliphatic side chain, were seen to be essential for diketopiperazine formation in addition to the more typical oxazolone structure formation, while blocking or removal of the τ-nitrogen did not change the b(2)(+) ion structures formed. Linear histidine analogues, DabA and KA, formed only diketopiperazine structures, suggesting that a steric interaction in the HisAla case may interfere with the complete trans-cis isomerization of the first amide bond that is necessary for diketopiperazine formation.
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Affiliation(s)
- Ashley C Gucinski
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, USA.
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Obolensky OI, Wu WW, Shen RF, Yu YK. Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:915-20. [PMID: 22396027 PMCID: PMC3468955 DOI: 10.1002/rcm.6180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
RATIONALE Peptide identification reliability can be improved by excluding from analysis those m/z peaks of candidate peptides which cannot be observed in practice due to various physical, chemical or thermodynamic considerations. We propose using dissociation energies (as opposed to proton affinities) as a predictor of observability of different m/z peaks in spectra of short peptides. METHODS Mass spectra of the tetrapeptides AAAA, AAFA, AAVA, AFAA, AVAA, AFFA, and AVVA were measured in the collision-induced dissociation (CID) activation mode on a grid of activation times 0.05 to 100 ms and normalized collision energy 10 to 35%. The lowest energy geometries and vibrational spectra were calculated for the precursor ions and their charged and neutral fragments using density functional theory (DFT) at the TPSS/6-31G(d,p) level. Dissociation energies were calculated for all fragmentation channels leading to b- or y-fragments. RESULTS It is demonstrated that m/z peaks observed in the mass spectra correspond to the fragmentation channels with the lowest dissociation energies. Using 50 kcal/mol as the cut-off value of dissociation energy, it was predicted that 28 out of 42 possible peaks in the b- and y-series of the seven tetrapeptides can be observed in mass spectra. In the experiments, 26 b- or y-peaks were observed, all of which are among the 28 predicted ones. CONCLUSIONS The use of dissociation energies generalizes the use of proton affinities for semi-quantitative predictions of relative intensities of different m/z peaks of short peptides. Further advances in this direction will pave the way for reliable quantitative predictions and, hence, for a significant improvement in robustness and accuracy of peptide and protein identification tools.
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Affiliation(s)
- O I Obolensky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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50
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Bernier MC, Paizs B, Wysocki VH. Influence of a Gamma Amino Acid on the Structures and Reactivity of Peptide a(3) Ions. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 316-318:259-267. [PMID: 23258959 PMCID: PMC3523335 DOI: 10.1016/j.ijms.2012.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Collision-induced dissociation of protonated AGabaAIG (where Gaba is gamma-amino butyric acid, NH(2)-(CH(2))(3)-COOH) leads to an unusually stable a(3) ion. Tandem mass spectrometry and theory are used here to probe the enhanced stability of this fragment, whose counterpart is not usually observed in CID of protonated peptides containing only alpha amino acids. Experiments are carried out on the unlabelled and (15)N-Ala labeled AGabaAIG (labeled separately at residue one or three) probing the b(3), a(3), a(3)-NH(3) (a(3) (*)), and b(2) fragments while theory is used to characterize the most stable b(3), a(3), and b(2) structures and the formation and dissociation of the a(3) ion. Our results indicate the AGabaA oxazolone b(3) isomer undergoes head-to-tail macrocyclization and subsequent ring opening to form the GabaAA sequence isomer while this chemistry is energetically disfavored for the AAA sequence. The AGabaA a(3) fragment also undergoes macrocyclization and rearrangement to form the rearranged imine-amide isomer while this reaction is energetically disfavored for the AAA sequence. The barriers to dissociation of the AGabaA a(3) ion via the a(3)→b(2) and a(3)→a(3)* channels are higher than the literature values reported for the AAA sequence. These two effects provide a clear explanation for the enhanced stability of the AGabaA a(3) ion.
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Affiliation(s)
- Matthew C. Bernier
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Bela Paizs
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
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