1
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Khawaja N, Hortal Sánchez L, O'Sullivan TR, Bloema J, Napoleoni M, Klenner F, Beinlich A, Hillier J, John T, Postberg F. Laboratory characterization of hydrothermally processed oligopeptides in ice grains emitted by Enceladus and Europa. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2024; 382:20230201. [PMID: 38736335 DOI: 10.1098/rsta.2023.0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/30/2024] [Indexed: 05/14/2024]
Abstract
The Cassini mission provided evidence for a global subsurface ocean and ongoing hydrothermal activity on Enceladus, based on results from Cassini's mass spectrometers. Laboratory simulations of hydrothermal conditions on icy moons are needed to further constrain the composition of ejected ice grains containing hydrothermally altered organic material. Here, we present results from our newly established facility to simulate the processing of ocean material within the temperature range 80-150°C and the pressure range 80-130 bar, representing conditions suggested for the water-rock interface on Enceladus. With this new facility, we investigate the hydrothermal processing of triglycine (GGG) peptide and, for the first time, analyse the extracted samples using laser-induced liquid beam ion desorption (LILBID) mass spectrometry, a laboratory analogue for impact ionization mass spectrometry of ice grains in space. We outline an approach to elucidate hydrothermally processed GGG in ice grains ejected from icy moons based on characteristic differences between GGG anion and cation mass spectra. These differences are linked to hydrothermal processing and thus provide a fingerprint of hydrothermal activity on extraterrestrial bodies. These results will serve as important guidelines for biosignatures potentially obtained by a future Enceladus mission and the SUrface Dust Analyzer (SUDA) instrument onboard Europa Clipper. This article is part of the theme issue 'Dust in the Solar System and beyond'.
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Affiliation(s)
- Nozair Khawaja
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
- Institute of Space Systems, University of Stuttgart , Stuttgart 70569, Germany
| | - Lucía Hortal Sánchez
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Thomas R O'Sullivan
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Judith Bloema
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Maryse Napoleoni
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Fabian Klenner
- Department of Earth and Space Sciences, University of Washington , Seattle, WA 98195, USA
| | - Andreas Beinlich
- Department of Mineralogy and Petrology, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Jon Hillier
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Timm John
- Department of Mineralogy and Petrology, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Frank Postberg
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, 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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3
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Yoshizawa K, Hirata K, Ishiuchi SI, Fujii M, Zehnacker A. Do Stereochemical Effects Overcome a Charge-Induced Perturbation in Isolated Protonated Cyclo(Tyr-Tyr)? J Phys Chem A 2022; 126:6387-6394. [PMID: 36098637 DOI: 10.1021/acs.jpca.2c03789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two diastereomers of the protonated diketopiperazine (DKP) dipeptide cyclo(Tyr-Tyr), namely, cyclo(LTyr-LTyr)H+ and cyclo(LTyr-DTyr)H+, are studied in a cryogenic ion trap by means of IR photodissociation spectroscopy combined with quantum chemical calculations. The two diastereomers have similar structures in which one of the rings is folded over the DKP ring and the other one is extended in a trans geometry, allowing a strong OH+···π interaction to take place. This contrasts to the observation of a stacked geometry for neutral cyclo(LTyr-LTyr) only under supersonic expansion conditions that do not exist for cyclo(LTyr-DTyr). In the protonated form, the strength of the OH+···π interaction is different for the two diastereomers, resulting in a ∼110 cm-1 difference in the ν(OH+) frequency and a smaller but clearly identifiable difference in the protonated amide ν(NH) frequency. Stereochemical effects are therefore still evidenced despite the strong perturbation due to the excess charge.
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Affiliation(s)
- Koki Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.,International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Anne Zehnacker
- International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.,Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, Orsay F-91405, France
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4
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Abstract
Protonated cyclic dipeptides undergo collision-induced dissociation, and this reaction mechanism strongly depends on the symmetry and the nature of the residues. We review the main dissociation mechanism for a series of cyclic dipeptides, obtained through chemical dynamics simulations. The systems range from the symmetrical cyclo-(glycyl-glycyl), with two possible symmetrical protonation sites located on the peptide ring, to cyclo-(tyrosyl-prolyl), where the symmetry of protonation sites on the peptide ring is broken by the dissimilar nature of the different residues. Finally, cyclo-(phenylalanyl-histidyl) shows a completely asymmetric situation, with the proton located on one of the dipeptide side chains, which explains the peculiar fragmentation mechanism induced by shuttling the proton, whose efficiency is strongly dependent on the relative chirality of the residues.
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5
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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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6
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Batoon P, Oomens J, Berden G, Ren J. Conformations of Protonated AlaDap and DapAla Characterized by IRMPD Spectroscopy and Molecular Modeling. J Phys Chem B 2018; 122:2191-2202. [DOI: 10.1021/acs.jpcb.7b10435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick Batoon
- Department
of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211, United States
| | - Jos Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jianhua Ren
- Department
of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211, United States
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7
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Alata I, Pérez-Mellor A, Ben Nasr F, Scuderi D, Steinmetz V, Gobert F, Jaïdane NE, Zehnacker-Rentien A. Does the Residues Chirality Modify the Conformation of a Cyclo-Dipeptide? Vibrational Spectroscopy of Protonated Cyclo-diphenylalanine in the Gas Phase. J Phys Chem A 2017; 121:7130-7138. [DOI: 10.1021/acs.jpca.7b06159] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivan Alata
- Institut
des Sciences Moléculaires d’Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Ariel Pérez-Mellor
- Institut
des Sciences Moléculaires d’Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Feriel Ben Nasr
- Institut
des Sciences Moléculaires d’Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
- Laboratoire
de Spectroscopie Atomique Moléculaire et Applications, Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Debora Scuderi
- Laboratoire
de Chimie Physique, CNRS, UMR8000, Univ. Paris-Sud, Orsay F-91405, France
| | - Vincent Steinmetz
- Laboratoire
de Chimie Physique, CNRS, UMR8000, Univ. Paris-Sud, Orsay F-91405, France
| | - Fabrice Gobert
- Laboratoire
de Chimie Physique, CNRS, UMR8000, Univ. Paris-Sud, Orsay F-91405, France
| | - Nejm-Eddine Jaïdane
- Laboratoire
de Spectroscopie Atomique Moléculaire et Applications, Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Anne Zehnacker-Rentien
- Institut
des Sciences Moléculaires d’Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
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8
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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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9
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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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10
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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11
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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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12
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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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13
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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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14
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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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15
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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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16
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Bouchoux G. From the mobile proton to wandering hydride ion: mechanistic aspects of gas-phase ion chemistry. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:505-518. [PMID: 23584944 DOI: 10.1002/jms.3204] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/06/2013] [Accepted: 03/06/2013] [Indexed: 06/02/2023]
Abstract
Structural characterization of molecular species by mass spectrometry supposes the knowledge of the type of ions generated and the mechanism by which they dissociate. In this context, a need for a rationalization of electrospray ionization(+)(-) mass spectra of small molecules has been recently expressed. Similarly, at the other end of the mass scale, efforts are currently made to interpret the major fragmentation processes of protonated and deprotonated peptides and their reduced forms produced in electron capture or electron transfer experiments. Most fragmentation processes of molecular and pseudo-molecular ions produced in the ion source of a mass spectrometer may be described by a combination of several key mechanistic steps: simple bond dissociation, formation of ion-neutral complex intermediates, hydrogen atom, hydride ion or proton migrations and nucleophilic attack. Selected crucial aspects of these elementary reactions, occurring inside positively charged ions, will be recalled and illustrated by examples taken in recent mass spectrometry literature. Emphasis will be given on the protonation process and its consequence in terms of structure and energetic.
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Affiliation(s)
- Guy Bouchoux
- Laboratoire des Mécanismes Réactionnels. Ecole Polytechnique. CNRS, Université Paris-sud, 91128, Palaiseau, France.
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17
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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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18
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Abstract
Analysis of drugs, biomarkers and their metabolites in tissue samples has always been an important aspect of the drug-development process. In the last decade, significant improvements in equipment and processes have made handling such samples far more efficient, with higher precision, accuracy and ruggedness. The purpose of this paper is to provide a primer for best practices of tissue analysis, including brief but specific tutorials on basic principles and laboratory operation. Included will be a discussion of what to consider when designing a study, tools available to make appropriate pre-study decisions, approaches for tissue acquisition and extraction, sample processing methods, and tips on creation of standards and QCs. We will offer some practical advice to help scientists who have good analytical skills, but are not experienced in tissue analysis to quickly start their own analyses with the minimum amount of time, labor and cost.
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19
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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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20
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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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21
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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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22
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Leavitt CM, Wolk AB, Fournier JA, Kamrath MZ, Garand E, Van Stipdonk MJ, Johnson MA. Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap. J Phys Chem Lett 2012; 3:1099-105. [PMID: 26288043 DOI: 10.1021/jz3003074] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Isomer-specific vibrational predissociation spectra are reported for the gas-phase GlySarH(+) and SarSarH(+) [Gly = glycine; Sar = sarcosine] ions prepared by electrospray ionization and tagged with weakly bound D2 adducts using a cryogenic ion trap. The contributions of individual isomers to the overlapping vibrational band patterns are completely isolated using a pump-probe photochemical hole-burning scheme involving two tunable infrared lasers and two stages of mass selection (hence IR(2)MS(2)). These patterns are then assigned by comparison with harmonic (MP2/6-311+G(d,p)) spectra for various possible conformers. Both systems occur in two conformations based on cis and trans configurations with respect to the amide bond. In addition to the usual single intramolecular hydrogen bond motif between the protonated amine and the nearby amide oxygen atom, cis-SarSarH(+) adopts a previous unreported conformation in which both amino NH's act as H-bond donors. The correlated red shifts in the NH donor and C═O acceptor components of the NH···O═C linkage to the acid group are unambiguously assigned in the double H-bonded conformer.
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Affiliation(s)
- Christopher M Leavitt
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Arron B Wolk
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Joseph A Fournier
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Michael Z Kamrath
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Etienne Garand
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Michael J Van Stipdonk
- ‡Department of Chemistry, Lawrence University, 711 East Boldt Way, Appleton, Wisconsin 54911, United States
| | - Mark A Johnson
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
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23
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Tirado M, Rutters J, Chen X, Yeung A, van Maarseveen J, Eyler JR, Berden G, Oomens J, Polfer NC. Disfavoring macrocycle b fragments by constraining torsional freedom: the "twisted" case of QWFGLM b6. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:475-482. [PMID: 22219043 DOI: 10.1007/s13361-011-0315-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/02/2011] [Accepted: 12/04/2011] [Indexed: 05/31/2023]
Abstract
While recent studies have shown that for some peptides, such as oligoglycines and Leu-enkephalin, mid-sized b fragment ions exist as a mixture of oxazolone and macrocycle structures, other primary structure motifs, such as QWFGLM, are shown to exclusively give rise to macrocycle structures. The aim of this study was to determine if certain amino acid residues are capable of suppressing macrocycle formation in the corresponding b fragment. The residues proline and 4-aminomethylbenzoic acid (4AMBz) were chosen because of their intrinsic rigidity, in the expectation that limited torsional flexibility may impede "head-to-tail" macrocycle formation. The presence of oxazolone versus macrocycle b(6) fragment structures was validated by infrared multiple photon dissociation (IRMPD) spectroscopy, using the free electron laser FELIX. It is confirmed that proline disfavors macrocycle formation in the cases of QPWFGLM b(7) and in QPFGLM b(6). The 4AMBz substitution experiments show that merely QWFG(4AMBz)M b(6), with 4AMBz in the fifth position, exhibits a weak oxazolone band. This effect is likely ascribed to a stabilization of the oxazolone structure, due to an extended oxazolone ring-phenyl π-electron system, not due to the rigidity of the 4AMBz residue. These results show that some primary structures have an intrinsic propensity to form macrocycle structures, which is difficult to disrupt, even using residues with limited torsional flexibility.
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Affiliation(s)
- Marcus Tirado
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
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24
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Leavitt CM, Wolk AB, Kamrath MZ, Garand E, Van Stipdonk MJ, Johnson MA. Characterizing the intramolecular H-bond and secondary structure in methylated GlyGlyH+ with H2 predissociation spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1941-1952. [PMID: 21952771 DOI: 10.1007/s13361-011-0228-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/03/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
We report vibrational predissociation spectra of the four protonated dipeptides derived from glycine and sarcosine, GlyGlyH(+)•(H(2))(1,2), GlySarH(+)•(D(2))(2), SarGlyH(+)•(H(2))(2), and SarSarH(+)•(D(2))(2), generated in a cryogenic ion trap. Sharp bands were recovered by monitoring photoevaporation of the weakly bound H(2) (D(2)) molecules in a linear action regime throughout the 700-4200 cm(-1) range using a table-top laser system. The spectral patterns were analyzed in the context of the low energy structures obtained from electronic structure calculations. These results indicate that all four species are protonated on the N-terminus, and feature an intramolecular H-bond involving the amino group. The large blue-shift in the H-bonded N-H fundamental upon incorporation of a methyl group at the N-terminus indicates that this modification significantly lowers the strength of the intramolecular H-bond. Methylation at the amide nitrogen, on the other hand, induces a significant rotation (~110°) about the peptide backbone.
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Affiliation(s)
- Christopher M Leavitt
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
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25
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Chen X, Tirado M, Steill JD, Oomens J, Polfer NC. Cyclic peptide as reference system for b ion structural analysis in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1011-1015. [PMID: 22012667 DOI: 10.1002/jms.1982] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Infrared multiple photon dissociation spectroscopy and hydrogen/deuterium exchange methods are used to confirm the macrocylic structure of a b(6) peptide fragment by direct comparison with a synthetically made cyclic peptide. The acetylation of the peptide N-terminus results in the inhibition of the macrocyclic formation, supporting the "head-to-tail" cyclization mechanism. Differences in hydrogen/deuterium exchange rates for macrocyclic and oxazalone structure peptide fragments are interpreted to be a result of the complex interplay of multiple basic sites in the peptide fragment, supporting the relay mechanism for deuterium exchange with CH(3)OD.
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Affiliation(s)
- Xian Chen
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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26
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Sinha RK, Erlekam U, Bythell BJ, Paizs B, Maître P. Diagnosing the protonation site of b2 peptide fragment ions using IRMPD in the X-H (X = O, N, and C) stretching region. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1645-1650. [PMID: 21953267 DOI: 10.1007/s13361-011-0173-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 05/17/2011] [Accepted: 05/19/2011] [Indexed: 05/31/2023]
Abstract
Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b(2) ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800-3800 cm(-1) range acquired on a table-top laser system. Combining this tunable laser with a high power CO(2) laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm(-1), corresponding to the asymmetric N-H stretch of the (nonprotonated) N-terminal NH(2) group, is a distinct vibrational signature of the ring-protonated oxazolone structure.
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Affiliation(s)
- Rajeev K Sinha
- Laboratoire de Chimie Physique, Université Paris Sud, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405, Orsay Cedex, France
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