1
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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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2
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Tang WK, Mu X, Li M, Martens J, Berden G, Oomens J, Chu IK, Siu CK. Formation of n → π + interaction facilitating dissociative electron transfer in isolated tyrosine-containing molecular peptide radical cations. Phys Chem Chem Phys 2021; 22:21393-21402. [PMID: 32940309 DOI: 10.1039/d0cp00533a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Long-range electron transfer in proteins can be rationalized as a sequential short-distance electron-hopping processes via amino acid residues having low ionization energy as relay stations. Tyrosine residues can serve as such redox-active intermediates through one-electron oxidation to form a π-radical cation at its phenol side chain. An electron transfer from a vicinal functional group to this π-electron hole completes an elementary step of charge migration. However, transient oxidized/reduced intermediates formed at those relay stations during electron transfer processes have not been observed. In this study, formation of analog reactive intermediates via electron donor-acceptor coupling is observed by using IRMPD action spectroscopy. An elementary charge migration at the molecular level in model tyrosine-containing peptide radical cations [M]˙+ in the gas phase is revealed with its unusual Cα-Cβ bond cleavage at the side chain of the N-terminal residue. This reaction is induced by the radical character of the N-terminal amino group (-NH2˙+) resulting from an n → π+ interaction between the nonbonding electron pair of NH2 (n) and the π-electron hole at the Tyr side chain (π+). The formation of -NH2˙+ is supported by the IRMPD spectrum showing a characteristic NH2 scissor vibration coupled with Tyr side-chain stretches at 1577 cm-1. This n → π+ interaction facilitates a dissociative electron transfer with NH2 as the relay station. The occurrence of this side-chain cleavage may be an indicator of the formation of reactive conformers featuring the n → π+ interaction.
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Affiliation(s)
- Wai Kit Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China.
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3
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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: 3] [Impact Index Per Article: 0.8] [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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4
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Ren J, Tian Y, Hossain E, Ho JS, Mann YS, Zhang Y, Browne MD, Connolly MD, Zuckermann RN. Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids. Biopolymers 2020; 111:e23358. [DOI: 10.1002/bip.23358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Jianhua Ren
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuan Tian
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Ekram Hossain
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Joshua S. Ho
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yadwinder S. Mann
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuntao Zhang
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Browne
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Connolly
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
| | - Ronald N. Zuckermann
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
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5
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Lam KHB, Lau JKC, Lai CK, Chu IK, Martens J, Berden G, Oomens J, Hopkinson AC, Siu KWM. Loss of water from protonated polyglycines: interconversion and dissociation of the product imidazolone ions. Phys Chem Chem Phys 2018; 20:18688-18698. [DOI: 10.1039/c8cp02543f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Imidazolones formed from polyglycines are located at the centre of the peptide backbone and dissociate more easily than interconvert.
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Affiliation(s)
- K. H. Brian Lam
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
| | - Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
- Department of Chemistry and Biochemistry
| | - Cheuk-Kuen Lai
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
| | - Ivan K. Chu
- Department of Chemistry
- The University of Hong Kong
- China
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
- Department of Chemistry and Biochemistry
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6
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Lam KHB, Lau JKC, Lai CK, Hopkinson AC, Siu KWM. Interconversion between 4-Imidazolone Ions; Isomers of [b 4] + Derived from Protonated Tetraglycine. J Phys Chem B 2017; 121:9541-9547. [PMID: 28945091 DOI: 10.1021/acs.jpcb.7b07586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Collision-induced dissociations of isotopically labeled protonated tetraglycines establish that the [b4]+ ion formed by loss of water from the second amide bond (structure II) rearranges to form N1-protonated 3,5-dihydro-4H-imidazol-4-one (structure I), the product of water loss from the first amide bond. Structure II is slightly higher in energy than I (ΔH at 0 K is 5.1 kJ mol-1, as calculated at M06-2X/6-311++G-(d,p)), and the barrier to interconversion is 139.8 kJ mol-1 above I. The dominant dissociation pathway is the loss of methanimine (HN=CH2) from ion I with a barrier of 167.1 kJ mol-1, giving [GlyGlyGlyGly + H - H2O - HN=CH2]+, ion III; a minor channel, loss of NH3, has a slightly higher barrier (181.5 kJ mol-1). Using labeled glycine (13Cα) it was determined that loss of the imine is from the same residue as that from which water was initially lost. The collision-induced dissociation spectra of ion III derived from both I and II were identical, and their energy-resolved curves were also very similar. Ion III fragments by losses of a glycine molecule (the dominant channel), a water molecule, and a glycine residue (57 Da), giving ions IV, V, and VII, respectively. Isotopic labeling established the origins of each of the neutral molecules that are lost. Using glycine (2,2 D2), rapid deuterium exchange was observed for both ions I and II for the α-hydrogens that are from the same residue as that from which the water had been eliminated.
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Affiliation(s)
- K H Brian Lam
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , 4700 Keele Street, Toronto, ON M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor , 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| | - Cheuk-Kuen Lai
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , 4700 Keele Street, Toronto, ON M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor , 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
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7
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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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8
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Bythell BJ, Abutokaikah MT, Wagoner AR, Guan S, Rabus JM. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:688-703. [PMID: 27896699 DOI: 10.1007/s13361-016-1530-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/04/2023]
Abstract
We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms. Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies. Graphical Abstract ᅟ.
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Affiliation(s)
- Benjamin J Bythell
- 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
| | - Ashley R Wagoner
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Jordan M Rabus
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
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9
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Schwob L, Lalande M, Egorov D, Rangama J, Hoekstra R, Vizcaino V, Schlathölter T, Poully JC. Radical-driven processes within a peptidic sequence of type I collagen upon single-photon ionisation in the gas phase. Phys Chem Chem Phys 2017; 19:22895-22904. [DOI: 10.1039/c7cp03376a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Radical creation after single-photon ionisation of collagen peptides induces the loss of molecules from amino-acid residue side-chains.
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Affiliation(s)
- Lucas Schwob
- CIMAP
- UMP 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Mathieu Lalande
- CIMAP
- UMP 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Jimmy Rangama
- CIMAP
- UMP 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Violaine Vizcaino
- CIMAP
- UMP 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
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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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11
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Lai CK, Mu X, Hao Q, Hopkinson AC, Chu IK. Formation, isomerization, and dissociation of ε- and α-carbon-centered tyrosylglycylglycine radical cations. Phys Chem Chem Phys 2014; 16:24235-43. [DOI: 10.1039/c4cp03119a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CID spectra of [Yε˙GG]+ and [YGGα˙]+ are identical, showing that interconversion occurs prior to dissociation. For [Yε˙GG]+, [Yπ˙GG]+ and [YGα˙G]+, the dissociation products are all distinctly different, indicating that dissociation occurs more readily than isomerization.
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Affiliation(s)
- Cheuk-Kuen Lai
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, China
| | - Xiaoyan Mu
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, China
| | - Qiang Hao
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, China
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto, Canada
| | - Ivan K. Chu
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, China
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12
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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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13
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Banu L, Blagojevic V, Bohme DK. Locating Pb2+ and Zn2+ in zinc finger-like peptides using mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1534-1542. [PMID: 23907592 DOI: 10.1007/s13361-013-0682-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/08/2013] [Accepted: 05/12/2013] [Indexed: 06/02/2023]
Abstract
The binding preferences of Pb(2+)and Zn(2+) in doubly charged complexes with zinc finger-like 12-residue peptides (Pep), [Mn(Pep-2(n-1)H)](2+) have been explored using tandem mass spectrometry. The peptides were synthesized strategically by blocking the N-terminus with an acetyl group and with four cysteine and/or histidine residues in positions 2, 5, 8, and 11, arranged in different motifs: CCHH, CHCH, and CCCC. The MS(2) spectra of the Pb(2+) and Zn(2+) complexes show multiple losses of water and a single methane loss and these provide a sensitive method for locating the metal dication and so elucidating its coordination. The elimination of a methane molecule indicated the position of the metal at the Cys2 residue. Whereas lead was observed to preferentially bind to cysteine residues, zinc was found to primarily bind to histidine residues and secondarily to cysteine residues. Preferential binding of lead to cysteine is preserved in the complexes with more than one Pb(2+). Key to the mechanism of the loss of water and methane is the metal dication withdrawing electrons from the proximal amidic nitrogen. This acidic nitrogen loses its hydrogen to an amidic oxygen situated four atoms away leading to formation of a five-member ring and the elimination of water.
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Affiliation(s)
- Laura Banu
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3, Canada
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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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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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Kilpatrick LE, Neta P, Yang X, Simón-Manso Y, Liang Y, Stein SE. Formation of y + 10 and y + 11 ions in the collision-induced dissociation of peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:655-663. [PMID: 22161574 DOI: 10.1007/s13361-011-0277-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 10/07/2011] [Accepted: 10/12/2011] [Indexed: 05/31/2023]
Abstract
Tandem mass spectra of peptide ions, acquired in shotgun proteomic studies of selected proteins, tissues, and organisms, commonly include prominent peaks that cannot be assigned to the known fragmentation product ions (y, b, a, neutral losses). In many cases these persist even when creating consensus spectra for inclusion in spectral libraries, where it is important to determine whether these peaks represent new fragmentation paths or arise from impurities. Using spectra from libraries and synthesized peptides, we investigate a class of fragment ions corresponding to y(n-1) + 10 and y(n-1) + 11, where n is the number of amino acid residues in the peptide. These 10 and 11 Da differences in mass of the y ion were ascribed before to the masses of [+ CO - H(2)O] and [+ CO - NH(3)], respectively. The mechanism is suggested to involve dissociation of the N-terminal residue at the CH-CO bond following loss of H(2)O or NH(3). MS(3) spectra of these ions show that the location of the additional 10 or 11 Da is at the N-terminal residue. The y(n-1) + 10 ion is most often found in peptides with N-terminal proline, asparagine, and histidine, and also with serine and threonine in the adjacent position. The y(n-1) + 11 ion is observed predominantly with histidine and asparagine at the N-terminus, but also occurs with asparagine in positions two through four. The intensities of the y(n-1) + 10 ions decrease with increasing peptide length. These data for y(n-1) + 10 and y(n-1) + 11 ion formation may be used to improve peptide identification from tandem mass spectra.
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Affiliation(s)
- Lisa E Kilpatrick
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, 100 Bureau Drive, MS8320, Gaithersburg, MD 20899, USA.
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