51
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Nguyen HTH, Shaffer CJ, Tureček F. Probing peptide cation-radicals by near-UV photodissociation in the gas phase. Structure elucidation of histidine radical chromophores formed by electron transfer reduction. J Phys Chem B 2015; 119:3948-61. [PMID: 25688483 DOI: 10.1021/jp511717c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Electron transfer reduction of gas-phase ions generated from histidine-containing peptides forms stable cation-radicals that absorb light at 355 nm, as studied for AAHAR, AAHAK, DSHAK, FHEK, HHGYK, and HHSHR. Laser photodissociation of mass-selected cation-radicals chiefly resulted in loss of H atoms, contrasting dissociations induced by slow collisional heating. The 355 nm absorption was due to new chromophores created by electron transfer and radical rearrangements in the cation-radicals. The chromophores were identified by time-dependent density functional theory calculations as 2H,3H-imidazoline and 2H-dihydrophenol radicals, formed by hydrogen atom transfer to the histidine and tyrosine side chain groups, respectively. These radicals undergo facile C-H bond dissociations upon photon absorption. In contrast, dissociations of histidine peptide cation-radicals containing the 1H,3H-imidazoline ring prefer loss of 4-methylimidazole via a multistep reaction pathway. The isomeric cation-radicals can be distinguished by a combination of collision-induced dissociation and near-UV photodissociation. The TD-DFT excitation energies in model imidazoline radicals were benchmarked on EOM-CCSD energies, and a satisfactory agreement was found for the M06-2X and ωB97XD functionals. The combination of electron transfer, photodissociation, collisional activation, and theory is presented as a powerful tool for studying structures and electronic properties of peptide cation-radicals in the gas phase.
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Affiliation(s)
- Huong T H Nguyen
- Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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52
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Calvo F. Atomistic Modeling of IR Action Spectra Under Circularly Polarized Electromagnetic Fields: Toward Action VCD Spectra. Chirality 2015; 27:253-61. [DOI: 10.1002/chir.22421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/06/2014] [Accepted: 11/28/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Florent Calvo
- Laboratoire Interdisciplinaire de Physique; Université Joseph Fourier; Grenoble France
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53
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Doussineau T, Paletto P, Dugourd P, Antoine R. Multiphoton dissociation of electrosprayed megadalton-sized DNA ions in a charge-detection mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:7-13. [PMID: 25348472 DOI: 10.1007/s13361-014-1011-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/17/2014] [Accepted: 09/20/2014] [Indexed: 06/04/2023]
Abstract
Charge detection mass spectrometry in combination with a linear electrostatic ion trap coupled to a continuous wavelength infrared CO2 laser has been used to study the multiphoton dissociation of DNA macromolecular ions. Samples, with masses ranging from 2.23 to 31.5 MDa, include single strand circular M13mp18, double strand circular M13mp18, and double strand linear LambdaPhage DNA fragments. Their activation energies for unimolecular dissociation were determined. Activation energy values slightly increase as a function of the molecular weight. The most important result is the difference between the fragmentations observed for hybridized double-strands and dimers of single strands.
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Affiliation(s)
- Tristan Doussineau
- Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
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54
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Zabuga AV, Kamrath MZ, Boyarkin OV, Rizzo TR. Fragmentation mechanism of UV-excited peptides in the gas phase. J Chem Phys 2014; 141:154309. [DOI: 10.1063/1.4897158] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aleksandra V. Zabuga
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Z. Kamrath
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, 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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55
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Brodbelt JS. Photodissociation mass spectrometry: new tools for characterization of biological molecules. Chem Soc Rev 2014; 43:2757-83. [PMID: 24481009 PMCID: PMC3966968 DOI: 10.1039/c3cs60444f] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.
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56
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Fraschetti C, Filippi A, Borocci S, Steinmetz V, Speranza M. Isomerism of Cycloserine and Its Protonated Form. Chempluschem 2014; 79:584-591. [DOI: 10.1002/cplu.201400006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 11/09/2022]
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57
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Webber N, He Y, Reilly JP. 157 nm photodissociation of dipeptide ions containing N-terminal arginine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:196-203. [PMID: 24310819 DOI: 10.1007/s13361-013-0762-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
Twenty singly-charged dipeptide ions with N-terminal arginine were photodissociated using 157 nm light in both a linear ion-trap mass spectrometer and a MALDI-TOF-TOF mass spectrometer. Analogous to previous work on dipeptides containing C-terminal arginine, this set of samples enabled insights into the photofragmentation propensities associated with individual residues. In addition to familiar products such as a-, d-, and immonium ions, m2 and m2+13 ions were also observed. Certain side chains tended to cleave between their β and γ carbons without necessarily forming d- or w-type ions, and a few other ions were produced by the high-energy fragmentation of multiple bonds.
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Affiliation(s)
- Nathaniel Webber
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
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58
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A review of electron-capture and electron-transfer dissociation tandem mass spectrometry in polymer chemistry. Anal Chim Acta 2014; 808:44-55. [DOI: 10.1016/j.aca.2013.09.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/03/2013] [Accepted: 09/18/2013] [Indexed: 01/24/2023]
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59
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Hu Y, Guan J, Bernstein ER. Mass-selected IR-VUV (118 nm) spectroscopic studies of radicals, aliphatic molecules, and their clusters. MASS SPECTROMETRY REVIEWS 2013; 32:484-501. [PMID: 24122973 DOI: 10.1002/mas.21387] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 06/02/2023]
Abstract
Mass-selected IR plus UV/VUV spectroscopy and mass spectrometry have been coupled into a powerful technique to investigate chemical, physical, structural, and electronic properties of radicals, molecules, and clusters. Advantages of the use of vacuum ultraviolet (VUV) radiation to create ions for mass spectrometry are its application to nearly all compounds with ionization potentials below the energy of a single VUV photon, its circumventing the requirement of UV chromophore group, its inability to ionize background gases, and its greatly reduced fragmenting capabilities. In this review, mass-selected IR plus VUV (118 nm) spectroscopy is introduced first in a general manner. Selected application examples of this spectroscopy are presented, which include the detections and structural analysis of radicals, molecules, and molecular clusters in a supersonic jet.
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Affiliation(s)
- Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
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60
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Robotham SA, Kluwe C, Cannon JR, Ellington A, Brodbelt JS. De novo sequencing of peptides using selective 351 nm ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:9832-8. [PMID: 24050806 DOI: 10.1021/ac402309h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although in silico database search methods remain more popular for shotgun proteomics methods, de novo sequencing offers the ability to identify peptides derived from proteins lacking sequenced genomes and ones with subtle splice variants or truncations. Ultraviolet photodissociation (UVPD) of peptides derivatized by selective attachment of a chromophore at the N-terminus generates a characteristic series of y ions. The UVPD spectra of the chromophore-labeled peptides are simplified and thus amenable to de novo sequencing. This method resulted in an observed sequence coverage of 79% for cytochrome C (eight peptides), 47% for β-lactoglobulin (five peptides), 25% for carbonic anhydrase (six peptides), and 51% for bovine serum albumin (33 peptides). This strategy also allowed differentiation of proteins with high sequence homology as evidenced by de novo sequencing of two variants of green fluorescent protein.
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Affiliation(s)
- Scott A Robotham
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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61
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Cotham VC, Wine Y, Brodbelt JS. Selective 351 nm photodissociation of cysteine-containing peptides for discrimination of antigen-binding regions of IgG fragments in bottom-up liquid chromatography-tandem mass spectrometry workflows. Anal Chem 2013; 85:5577-85. [PMID: 23641966 DOI: 10.1021/ac400851x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite tremendous inroads in the development of more sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategies for mass spectrometry-based proteomics, there remains a significant need for enhancing the selectivity of MS/MS-based workflows for streamlined analysis of complex biological mixtures. Here, a novel LC-MS/MS platform based on 351 nm ultraviolet photodissociation (UVPD) is presented for the selective analysis of cysteine-peptide subsets in complex protein digests. Cysteine-selective UVPD is mediated through the site-specific conjugation of reduced cysteine residues with a 351 nm active chromogenic Alexa Fluor 350 (AF350) maleimide tag. Only peptides containing the AF350 chromophore undergo photodissociation into extensive arrays of b- and y-type fragment ions, thus providing a facile means for differentiating cysteine-peptide targets from convoluting peptide backgrounds. With the use of this approach in addition to strategic proteolysis, the selective analysis of diagnostic heavy-chain complementarity determining regions (CDRs) of single-chain antibody (scAb) fragments is demonstrated.
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Affiliation(s)
- Victoria C Cotham
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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62
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Parneix P, Basire M, Calvo F. Accurate modeling of infrared multiple photon dissociation spectra: the dynamical role of anharmonicities. J Phys Chem A 2013; 117:3954-9. [PMID: 23581979 DOI: 10.1021/jp402459f] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamical response of a molecular system to a macropulse typically produced by a free-electron laser is theoretically modeled over experimentally long times, within a realistic kinetic Monte Carlo framework that incorporates absorption, stimulated emission, spontaneous emission, and dissociation events. The simulation relies on an anharmonic potential energy surface obtained from quantum chemistry calculations. Application to cationic naphthalene yields a better agreement with measurements than the anharmonic linear absorption spectrum, thus emphasizing the importance of specific dynamical effects on the spectral properties.
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Affiliation(s)
- Pascal Parneix
- Institut des Sciences Moléculaires d'Orsay, UMR CNRS 8214, Université Paris Sud 11, Bât. 210, F91405 Orsay Cedex, France.
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63
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He Y, Webber N, Reilly JP. 157 nm photodissociation of a complete set of dipeptide ions containing C-terminal arginine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:675-683. [PMID: 23378257 DOI: 10.1007/s13361-012-0514-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/17/2012] [Accepted: 07/18/2012] [Indexed: 06/01/2023]
Abstract
Twenty singly-charged dipeptide ions with C-terminal arginine were photodissociated with 157 nm light and their tandem mass spectra recorded. Many of the small product ions that were observed are standard peptide fragments that have been commonly seen in VUV photodissociation studies. However, the study of a library of dipeptides containing all 20 N-terminal amino acids enabled the recognition of trends associated with the occurrence of w-, v-, and immonium ions, the observation of competition between forming N- and C-terminal fragments in dipeptide RR, and the identification of some unusual fragment ions appearing at masses of 183, 187, 196, and 197 Da. A highly accurate internal calibration of the photodissociation TOF-TOF data enabled molecular formulae for these four product ions to be derived. Their proposed structures reflect the rather high-energy nature of this fragmentation phenomenon.
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Affiliation(s)
- Yi He
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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64
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Xu Z, Shaw JB, Brodbelt JS. Comparison of MS/MS methods for characterization of DNA/cisplatin adducts. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:265-273. [PMID: 23264150 PMCID: PMC3570664 DOI: 10.1007/s13361-012-0532-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/01/2012] [Accepted: 11/01/2012] [Indexed: 06/01/2023]
Abstract
The development of activation/dissociation techniques such as ultraviolet photodissociation (UVPD), infrared multiphoton dissociation (IRMPD), and electron transfer dissociation (ETD) as alternatives to collision induced dissociation (CID) has extended the range of strategies for characterizing biologically relevant molecules. Here, we describe a comprehensive comparison of CID, IRMPD, UVPD, ETD, and hybrid processes termed ETcaD and ET-IRMPD (and analogous hybrid methods in the negative mode NETcaD and NET-IRMPD) for generating sequence-specific fragment ions and allowing adduction sites to be pinpointed for DNA/cisplatin adducts. Among the six MS/MS methods, the numerous products generated by the IRMPD and UVPD techniques resulted in the most specific and extensive backbone cleavages. We conclude that IRMPD and UVPD methods generally offer the best characteristics for pinpointing the cisplatin adduction sites in the fragment-rich spectra.
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65
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Zhou X, Cui J, Li ZH, Wang G, Liu Z, Zhou M. Carbonyl Bonding on Oxophilic Metal Centers: Infrared Photodissociation Spectroscopy of Mononuclear and Dinuclear Titanium Carbonyl Cation Complexes. J Phys Chem A 2013; 117:1514-21. [DOI: 10.1021/jp3120429] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiaojie Zhou
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai 200433, China
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66
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Interaction of Cisplatin with Adenine and Guanine: A Combined IRMPD, MS/MS, and Theoretical Study. J Am Chem Soc 2013; 135:1445-55. [DOI: 10.1021/ja309857d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Debora Scuderi
- Laboratoire de Chimie-Physique, Université Paris Sud Orsay, Avenue Georges Clémenceau,
91405 Orsay Cedex, France
- CNRS-UMR 8000
| | - Jean-Yves Salpin
- Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation
pour la Biologie et l’Environnement, Boulevard François
Mitterrand, 91025 Evry, France
- CNRS-UMR 8587
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67
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Van Riper SK, de Jong EP, Carlis JV, Griffin TJ. Mass Spectrometry-Based Proteomics: Basic Principles and Emerging Technologies and Directions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 990:1-35. [DOI: 10.1007/978-94-007-5896-4_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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68
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Liu J, McLuckey SA. Electron Transfer Dissociation: Effects of Cation Charge State on Product Partitioning in Ion/Ion Electron Transfer to Multiply Protonated Polypeptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 330-332:174-181. [PMID: 23264749 PMCID: PMC3525064 DOI: 10.1016/j.ijms.2012.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The effect of cation charge state on product partitioning in the gas-phase ion/ion electron transfer reactions of multiply protonated tryptic peptides, model peptides, and relatively large peptides with singly charged radical anions has been examined. In particular, partitioning into various competing channels, such as proton transfer (PT) versus electron transfer (ET), electron transfer with subsequent dissociation (ETD) versus electron transfer with no dissociation (ET,noD), and fragmentation of backbone bonds versus fragmentation of side chains, was measured quantitatively as a function of peptide charge state to allow insights to be drawn about the fundamental aspects of ion/ion reactions that lead to ETD. The ET channel increases relative to the PT channel, ETD increases relative to ET,noD, and fragmentation at backbone bonds increases relative to side-chain cleavages as cation charge state increases. The increase in ET versus PT with charge state is consistent with a Landau-Zener based curve-crossing model. An optimum charge state for ET is predicted by the model for the ground state-to-ground state reaction. However, when the population of excited product ion states is considered, it is possible that a decrease in ET efficiency as charge state increases will not be observed due to the possibility of the population of excited electronic states of the products. Several factors can contribute to the increase in ETD versus ET,noD and backbone cleavage versus side-chain losses. These factors include an increase in reaction exothermicity and charge state dependent differences in precursor and product ion structures, stabilities, and sites of protonation.
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Affiliation(s)
| | - Scott A. McLuckey
- Address reprint requests to: Dr. S.A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084, Phone: (765) 494-5270, Fax: (765) 494-0239,
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69
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Dodds ED. Gas-phase dissociation of glycosylated peptide ions. MASS SPECTROMETRY REVIEWS 2012; 31:666-82. [PMID: 22407588 DOI: 10.1002/mas.21344] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 12/22/2011] [Accepted: 12/27/2011] [Indexed: 05/15/2023]
Abstract
Among the myriad of protein post-translational modifications (PTMs), glycosylation presents a singular analytical challenge. On account of the extraordinary diversity of protein-linked carbohydrates and the great complexity with which they decorate glycoproteins, the rigorous establishment of glycan-protein connectivity is often an arduous experimental venture. Consequently, elaborating the interplay between structures of oligosaccharides and functions of proteins they modify is usually not a straightforward task. A more mature biochemical appreciation of carbohydrates as PTMs will significantly hinge upon analytical advances in the field of glycoproteomics. Undoubtedly, the analysis of glycosylated peptides by tandem mass spectrometry (MS/MS) will play a pivotal role in this regard. The goal of this review is to summarize, from an analytical and tutorial perspective, the present state of knowledge regarding the dissociation of glycopeptide ions as accomplished by various MS/MS methods. In addition, this review will endeavor to harmonize some seemingly disparate findings to provide a more complete and broadly applicable description of glycopeptide ion fragmentation. A fuller understanding of the rich variety of glycopeptide dissociation behaviors will allow glycoproteomic researchers to maximize the information yielded by MS/MS experiments, while also paving the way to new innovations in MS-based glycoproteomics.
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Affiliation(s)
- Eric D Dodds
- Department of Chemistry, University of Nebraska-Lincoln, 711 Hamilton Hall, Lincoln, Nebraska 68588-0304, USA.
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70
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Ko BJ, Brodbelt JS. Enhanced electron transfer dissociation of peptides modified at C-terminus with fixed charges. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1991-2000. [PMID: 22895859 DOI: 10.1007/s13361-012-0458-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/21/2012] [Accepted: 07/21/2012] [Indexed: 06/01/2023]
Abstract
The impact of the conversion of carboxylates in peptides to basic or fixed charge sites on the outcome of electron transfer dissociation (ETD) is evaluated with respect to ETD efficiency and the number of diagnostic sequence ions. Four reagents, including benzylamine (BA), 1-benzylpiperazine (BZP), carboxymethyl trimethylammonium chloride hydrazide (GT), and (2-aminoethyl)trimethylammonium chloride hydrochloride (AETMA), were used for the carboxylate derivatization, with the first two replacing the acidic carboxylate groups with basic functionalities and the latter two introducing fixed charge sites. The ETD efficiencies and Xcorr scores were compared for both nonderivatized and derivatized tryptic and Glu-C peptides from cytochrome c. Derivatization of the carboxylate increases the average charge states, the number of fragment ions, and the dissociation efficiencies of peptides, especially for the fixed charge reagent, AETMA.
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Affiliation(s)
- Byoung Joon Ko
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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71
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Yang G, Zhu R, Zhou L, Liu C. Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1372-1383. [PMID: 23019170 DOI: 10.1002/jms.3075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Calculations were performed to study the interactions of metal ions (M) with (multiple) amino acids (AA) and fill the gap between single AA and proteins. A complete conformational search results in nine and eleven ZnGly isomers at B3P86 and MP2 levels, respectively, and four populated conformers of glycine are responsible for production of these isomers. For all M, the isomers via the OO and NO binding modes are the main constituents, and the OO mode is favored by stronger electrostatic interactions. Binding with more glycines causes larger structural distortions, improves relative stabilities of monodentate binding isomers and generates new binding modes (e.g. ZnB(III) via only the hydroxyl group). The scaling factor of Zn(Gly)(n) structures, the ratio of its binding affinity versus the sum of comprising ZnGly isomers, is linear with glycine number (n), and the linear relationship may not be altered by mutations of glycines and M. It thus allows to estimate M(AA)(n) binding affinities (n ≥ 2) from the comprising MAA structures and analyze their structures with kinetic methods. The DFT and MP2 results become comparable by increasing metal coordination, e.g. the ZnB(III) versus ZnA(I) (zwitterionic) relative energy differs by 41.9 kcal mol(-1) at B3P86 and MP2 levels and is close by addition of three water molecules (4.1 kcal mol(-1)). The presence of water solvent improves the relative stabilities of monodentate binding isomers and results in a broader conformational distribution.
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Affiliation(s)
- Gang Yang
- Institute of Theoretical Chemistry, Shandong University, Jinan, P R China.
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72
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Cui J, Xing X, Chi C, Wang G, Liu Z, Zhou M. Infrared Photodissociation Spectra of Mass-Selected Homoleptic Dinuclear Palladium Carbonyl Cluster Cations in the Gas Phase. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201200595] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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73
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Bianco G, Lelario F, Battista FG, Bufo SA, Cataldi TRI. Identification of glucosinolates in capers by LC-ESI-hybrid linear ion trap with Fourier transform ion cyclotron resonance mass spectrometry (LC-ESI-LTQ-FTICR MS) and infrared multiphoton dissociation. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1160-1169. [PMID: 22972784 DOI: 10.1002/jms.2996] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
An liquid chromatography-mass spectrometry method using electrospray ionization in negative ion mode coupled with a hybrid quadrupole linear ion trap and Fourier transform ion cyclotron resonance (FTICR) mass spectrometer was applied to characterize of intact glucosinolates (GLSs) in crude sample extracts of wild bud flowers of Capparis spinosa (Capparis species, family Capparaceae). Structural information of GLSs was obtained upon precursor ions' isolation within the FTICR trapping cell and subsequent fragmentation induced by infrared multiphoton dissociation (IRMPD). Such a fragmentation was found very useful in terms of chemical identification of all precursor ions [M-H](-) including sulfur-rich GLSs reported here for the first time. Along with most common GLSs already found in capers such as glucocapparin, isopropyl/n-propyl-GLS, mercapto-glucocapparin, and two indolic GLS, i.e., 4-hydroxyglucobrassicin and glucobrassicin, the occurrence of the uncommon glycinyl-glucocapparin as well as two sulfur-rich GLSs is reported. IRMPD showed an increased selectivity towards disulfide bond cleavages with thiol migration, suggesting the side chain structure of non-targeted compounds, i.e., disulfanyl-glucocapparin and trisulfanyl-glucocapparin. Glucocapparin [2.05 ± 0.25 mg/g, dry weight (dw)] was the most abundant GLS, followed by glucobrassicin (232 ± 18 µg/g, dw) and 4-hydroxyglucobrassicin (89 ± 12 µg/g, dw). All other compounds were present at very low content ranging from 0.5 to 1.5 µg/g dw.
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Affiliation(s)
- Giuliana Bianco
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via dell'Ateneo Lucano, n° 10-85100, Potenza, Italy
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74
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Doussineau T, Antoine R, Santacreu M, Dugourd P. Pushing the Limit of Infrared Multiphoton Dissociation to Megadalton-Size DNA Ions. J Phys Chem Lett 2012; 3:2141-2145. [PMID: 26295761 DOI: 10.1021/jz300844e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report the use of infrared multiphoton dissociation (IRMPD) for the determination of relative activation energies for unimolecular dissociation of megadalton DNA ions. Single ions with masses in the megadalton range were stored in an electrostatic ion trap for a few tens of milliseconds and the image current generated by the roundtrips of ions in the trap was recorded. While being trapped, single ions were irradiated by a CO2 laser and fragmented, owing to multiphoton IR activation. The analysis of the single-ion image current during the heating period allows us to measure changes in the charge of the trapped ion. We estimated the activation energy associated with the dissociation of megadalton-size DNA ions in the frame of an Arrhenius-like model by analyzing a large set of individual ions in order to construct a frequency histogram of the dissociation rates for a collection of ions.
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Affiliation(s)
- Tristan Doussineau
- Université de Lyon, CNRS, UMR5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Rodolphe Antoine
- Université de Lyon, CNRS, UMR5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Marion Santacreu
- Université de Lyon, CNRS, UMR5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Philippe Dugourd
- Université de Lyon, CNRS, UMR5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
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75
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Ledvina AR, Lee MV, McAlister GC, Westphall MS, Coon JJ. Infrared multiphoton dissociation for quantitative shotgun proteomics. Anal Chem 2012; 84:4513-9. [PMID: 22480380 DOI: 10.1021/ac300367p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We modified a dual-cell linear ion trap mass spectrometer to perform infrared multiphoton dissociation (IRMPD) in the low-pressure trap of a dual-cell quadrupole linear ion trap (dual-cell QLT) and perform large-scale IRMPD analyses of complex peptide mixtures. Upon optimization of activation parameters (precursor q-value, irradiation time, and photon flux), IRMPD subtly, but significantly, outperforms resonant-excitation collisional-activated dissociation (CAD) for peptides identified at a 1% false-discovery rate (FDR) from a yeast tryptic digest (95% confidence, p = 0.019). We further demonstrate that IRMPD is compatible with the analysis of isobaric-tagged peptides. Using fixed QLT rf amplitude allows for the consistent retention of reporter ions, but necessitates the use of variable IRMPD irradiation times, dependent upon precursor mass to charge (m/z). We show that IRMPD activation parameters can be tuned to allow for effective peptide identification and quantitation simultaneously. We thus conclude that IRMPD performed in a dual-cell ion trap is an effective option for the large-scale analysis of both unmodified and isobaric-tagged peptides.
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Affiliation(s)
- Aaron R Ledvina
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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76
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Robinson MR, Madsen JA, Brodbelt JS. 193 nm ultraviolet photodissociation of imidazolinylated Lys-N peptides for de novo sequencing. Anal Chem 2012; 84:2433-9. [PMID: 22283738 DOI: 10.1021/ac203227y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The goal of many MS/MS de novo sequencing strategies is to generate a single product ion series that can be used to determine the precursor ion sequence. Most methods fall short of achieving such simplified spectra, and the presence of additional ion series impede peptide identification. The present study aims to solve the problem of confounding ion series by enhancing the formation of "golden" sets of a, b, and c ions for sequencing. Taking advantage of the characteristic mass differences between the golden ions allows N-terminal fragments to be readily identified while other ion series are excluded. By combining the use of Lys-N, an alternate protease, to produce peptides with lysine residues at each N-terminus with subsequent imidazolinylation of the ε-amino group of each lysine, peptides with highly basic sites localized at each N-terminus are generated. Subsequent MS/MS analysis by using 193 nm ultraviolet photodissociation (UVPD) results in enhanced formation of the diagnostic golden pairs and golden triplets that are ideal for de novo sequencing.
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Affiliation(s)
- Michelle R Robinson
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
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77
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Chi C, Cui J, Li ZH, Xing X, Wang G, Zhou M. Infrared photodissociation spectra of mass selected homoleptic dinuclear iron carbonyl cluster anions in the gas phase. Chem Sci 2012. [DOI: 10.1039/c2sc20119d] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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78
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Zhou W, Håkansson K. Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry. CURR PROTEOMICS 2011; 8:297-308. [PMID: 22389641 PMCID: PMC3289259 DOI: 10.2174/157016411798220826] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fourier transform tandem mass spectrometry (MS/MS) provides high mass accuracy, high sensitivity, and analytical versatility and has therefore emerged as an indispensable tool for structural elucidation of biomolecules. Glycosylation is one of the most common posttranslational modifications, occurring in ~50% of proteins. However, due to the structural diversity of carbohydrates, arising from non-template driven biosynthesis, achievement of detailed structural insight is highly challenging. This review briefly discusses carbohydrate sample preparation and ionization methods, and highlights recent developments in alternative high-resolution MS/MS strategies, including infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD), for carbohydrates with a focus on glycans and proteoglycans from mammalian glycoproteins.
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Affiliation(s)
- Wen Zhou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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79
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Zhou W, Håkansson K. Electron detachment dissociation of fluorescently labeled sialylated oligosaccharides. Electrophoresis 2011; 32:3526-35. [PMID: 22120881 DOI: 10.1002/elps.201100327] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 08/11/2011] [Accepted: 09/05/2011] [Indexed: 01/07/2023]
Abstract
We explored the application of electron detachment dissociation (EDD) and infrared multiphoton dissociation (IRMPD) tandem mass spectrometry to fluorescently labeled sialylated oligosaccharides. Standard sialylated oligosaccharides and a sialylated N-linked glycan released from human transferrin were investigated. EDD yielded extensive glycosidic cleavages and cross-ring cleavages in all cases studied, consistently providing complementary structural information compared with infrared multiphoton dissociation. Neutral losses and satellite ions such as C-2H ions were also observed following EDD. In addition, we examined the influence of different fluorescent labels. The acidic label 2-aminobenzoic acid (2-AA) enhanced signal abundance in negative-ion mode. However, few cross-ring fragments were observed for 2-AA-labeled oligosaccharides. The neutral label 2-aminobenzamide (2-AB) resulted in more cross-ring cleavages compared with 2-AA-labeled species, but not as extensive fragmentation as for native oligosaccharides, likely resulting from altered negative charge locations from introduction of the fluorescent tag.
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Affiliation(s)
- Wen Zhou
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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80
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Antoine R, Dugourd P. Visible and ultraviolet spectroscopy of gas phase protein ions. Phys Chem Chem Phys 2011; 13:16494-509. [PMID: 21811728 DOI: 10.1039/c1cp21531k] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.
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81
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Doussineau T, Bao CY, Clavier C, Dagany X, Kerleroux M, Antoine R, Dugourd P. Infrared multiphoton dissociation tandem charge detection-mass spectrometry of single megadalton electrosprayed ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:084104. [PMID: 21895258 DOI: 10.1063/1.3628667] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This work presents the implementation of tandem mass spectrometry for experiments on single electrosprayed ions from compounds of megadalton (MDa) molecular weight, using two charge detection devices. The first mass spectrometry stage (first charge detection device) combined with an ion gate allows both mass-to-charge ratio and charge selections of the megadalton ion of interest. The second stage is based on an electrostatic ion trap and consists of an image charge detection tube mounted between two ion mirrors. Single MDa ions can be stored for several dozen milliseconds. During the trapping time, single ions can be irradiated by a continuous wavelength CO(2) laser. We observe stepwise changes in the charge of a single trapped ion owing to multiphoton activation. Illustration of infrared multiphoton dissociation tandem mass spectrometry are given for single megadalton ions of poly(ethylene oxide)s and DNAs.
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82
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Beck JP, Lisy JM. Infrared spectroscopy of hydrated alkali metal cations: Evidence of multiple photon absorption. J Chem Phys 2011; 135:044302. [DOI: 10.1063/1.3609760] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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83
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Salpin JY, Guillaumont S, Ortiz D, Tortajada J, Maître P. Direct evidence for tautomerization of the uracil moiety within the Pb2+/uridine-5'-monophosphate complex: a combined tandem mass spectrometry and IRMPD study. Inorg Chem 2011; 50:7769-78. [PMID: 21744847 DOI: 10.1021/ic200918q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides.
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Affiliation(s)
- Jean-Yves Salpin
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonn e, Bâtiment Maupertuis, Boulevard François Mitterrand, 91025 Evry, France.
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84
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Wesdemiotis C, Solak N, Polce MJ, Dabney DE, Chaicharoen K, Katzenmeyer BC. Fragmentation pathways of polymer ions. MASS SPECTROMETRY REVIEWS 2011; 30:523-559. [PMID: 20623599 DOI: 10.1002/mas.20282] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 11/05/2009] [Accepted: 11/05/2009] [Indexed: 05/29/2023]
Abstract
Tandem mass spectrometry (MS/MS) is increasingly applied to synthetic polymers to characterize chain-end or in-chain substituents, distinguish isobaric and isomeric species, and determine macromolecular connectivities and architectures. For confident structural assignments, the fragmentation mechanisms of polymer ions must be understood, as they provide guidelines on how to deduce the desired information from the fragments observed in MS/MS spectra. This article reviews the fragmentation pathways of synthetic polymer ions that have been energized to decompose via collisionally activated dissociation (CAD), the most widely used activation method in polymer analysis. The compounds discussed encompass polystyrenes, poly(2-vinyl pyridine), polyacrylates, poly(vinyl acetate), aliphatic polyester copolymers, polyethers, and poly(dimethylsiloxane). For a number of these polymers, several substitution patterns and architectures are considered, and questions regarding the ionization agent and internal energy of the dissociating precursor ions are also addressed. Competing and consecutive dissociations are evaluated in terms of the structural insight they provide about the macromolecular structure. The fragmentation pathways of the diverse array of polymer ions examined fall into three categories, viz. (1) charge-directed fragmentations, (2) charge-remote rearrangements, and (3) charge-remote fragmentations via radical intermediates. Charge-remote processes predominate. Depending on the ionizing agent and the functional groups in the polymer, the incipient fragments arising by pathways (1)-(3) may form ion-molecule complexes that survive long enough to permit inter-fragment hydrogen atom, proton, or hydride transfers.
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Affiliation(s)
- Chrys Wesdemiotis
- Department of Chemistry, The University of Akron, OH 44325-3601, USA.
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85
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Madsen JA, Cullen TW, Trent MS, Brodbelt JS. IR and UV photodissociation as analytical tools for characterizing lipid A structures. Anal Chem 2011; 83:5107-13. [PMID: 21595441 PMCID: PMC3128199 DOI: 10.1021/ac103271w] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The utility of 193-nm ultraviolet photodissociation (UVPD) and 10.6-μm infrared multiphoton dissociation (IRMPD) for the characterization of lipid A structures was assessed in an ion trap mass spectrometer. The fragmentation behavior of lipid A species was also evaluated by activated-electron photodetachment (a-EPD), which uses 193-nm photons to create charge reduced radicals that are subsequently dissociated by collisional activation. In contrast to collision-induced dissociation (CID), IRMPD offered the ability to selectively differentiate product ions with varying degrees of phosphorylation because of the increased photoabsorption cross sections and thus dissociation of phosphate-containing species. Both 193-nm UVPD and a-EPD yielded higher abundances and a larger array of product ions arising from C-C cleavages, as well as cross-ring and inter-ring glucosamine cleavages, compared to CID and IRMPD, because of high energy, single-photon absorption, and/or radical-directed dissociation. UVPD at 193 nm also exhibited enhanced cleavage between the amine and carbonyl groups on the 2- and 2'-linked primary acyl chains. Lastly, UVPD of phosphorylethanolamine-modified lipid A species resulted in preferential cleavage of the C-O bond between ethanolamine and phosphate, enabling the selective identification of this modification.
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Affiliation(s)
- James A. Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
| | - Thomas W. Cullen
- Section of Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX, USA 78712
| | - M. Stephen Trent
- Section of Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX, USA 78712
- The Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA 78712
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
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86
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Palumbo AM, Smith SA, Kalcic CL, Dantus M, Stemmer PM, Reid GE. Tandem mass spectrometry strategies for phosphoproteome analysis. MASS SPECTROMETRY REVIEWS 2011; 30:600-25. [PMID: 21294150 DOI: 10.1002/mas.20310] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.
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Affiliation(s)
- Amanda M Palumbo
- Department of Chemistry, Michigan State University, East Lansing, USA
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87
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Vasicek LA, Ledvina AR, Shaw J, Griep-Raming J, Westphall MS, Coon JJ, Brodbelt JS. Implementing photodissociation in an Orbitrap mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1105-8. [PMID: 21953052 PMCID: PMC3202985 DOI: 10.1007/s13361-011-0119-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/28/2011] [Accepted: 03/01/2011] [Indexed: 05/25/2023]
Abstract
We modified a dual pressure linear ion trap Orbitrap to permit infrared multiphoton dissociation (IRMPD) in the higher energy collisional dissociation (HCD) cell for high resolution analysis. A number of parameters, including the pressures of the C-trap and HCD cell, the radio frequency (rf) amplitude applied to the C-trap, and the HCD DC offset, were evaluated to optimize IRMPD efficiency and maintain a high signal-to-noise ratio. IRMPD was utilized for characterization of phosphopeptides, supercharged peptides, and N-terminal modified peptides, as well as for top-down protein analysis. The high resolution and high mass accuracy capabilities of the Orbitrap analyzer facilitated confident assignment of product ions arising from IRMPD.
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Affiliation(s)
- Lisa A. Vasicek
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Aaron R. Ledvina
- Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Jared Shaw
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | | | - Michael S. Westphall
- Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Joshua J. Coon
- Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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88
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Kollipara S, Agarwal N, Varshney B, Paliwal J. Technological Advancements in Mass Spectrometry and Its Impact on Proteomics. ANAL LETT 2011. [DOI: 10.1080/00032719.2010.520386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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89
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Brodbelt JS. Shedding light on the frontier of photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:197-206. [PMID: 21472579 DOI: 10.1007/s13361-010-0023-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
The development of new ion activation/dissociation methods is motivated by the need for more versatile ways to characterize structures of ions, especially in the growing arena of biological mass spectrometry in which better tools for determining sequences, modifications, interactions, and conformations of biopolymers are essential. Although most agree that collision-induced dissociation (CID) remains the gold standard for ion activation/dissociation, recent inroads in electron- and photon-based activation methods have cemented their role as outstanding alternatives. This article will focus on the impact of photodissociation, including its strengths and drawbacks as an analytical tool, and its potential for further development in the next decade. Moreover, the discussion will emphasize photodissociation in quadrupole ion traps, because that platform has been used for one of the greatest arrays of new applications over the past decade.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.
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90
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Smith SI, Brodbelt JS. Characterization of oligodeoxynucleotides and modifications by 193 nm photodissociation and electron photodetachment dissociation. Anal Chem 2011; 82:7218-26. [PMID: 20681614 DOI: 10.1021/ac100989q] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet photodissociation (UVPD) at 193 nm is compared to collision induced dissociation (CID) for sequencing and determination of modifications of multideprotonated 6-20-mer oligodeoxynucleotides. UVPD at 193 nm causes efficient charge reduction of the deprotonated oligodeoxynucleotides via electron detachment, in addition to extensive backbone cleavages to yield sequence ions of relatively low abundance, including w, x, y, z, a, a-B, b, c, and d ions. Although internal ions populate UVPD spectra, base loss ions from the precursor are absent. Subsequent CID of the charge-reduced oligodeoxynucleotides formed upon electron detachment, in a net process called electron photodetachment dissociation (EPD), results in abundant sequence ions in terms of w, z, a, a-B, and d products, with a marked decrease in the abundance of precursor base loss ions and internal fragments. Complete sequencing was possible for virtually all oligodeoxynucleotides studied. EPD of three modified oligodeoxynucleotides, a methylated oligodeoxynucleotide, a phosphorothioate-modified oligodeoxynucleotide, and an ethylated-oligodeoxynucleotide, resulted in specific and extensive backbone cleavages, specifically, w, z, a, a-B, and d products, which allowed the modification site(s) to be pinpointed to a more specific location than by conventional CID.
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Affiliation(s)
- Suncerae I Smith
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
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91
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Ko BJ, Brodbelt JS. Ultraviolet photodissociation of carboxylate-derivatized peptides in a quadrupole ion trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:49-56. [PMID: 21472543 DOI: 10.1007/s13361-010-0016-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
The fragmentation patterns obtained by ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) in a quadrupole ion trap mass spectrometer were compared for peptides modified at their C-termini and at acidic amino acids. Attachment of Alexa Fluor 350 or 7-amino-4-methyl-coumarin chromophores at the C-terminal and acidic residues enhances the UV absorptivity of the peptides and all fragment ions that retain the chromophore, such as the y ions that contain the chromophore-modified C-terminus. Whereas CID results in the formation of the typical array of mainly y-type and a/b-type fragment ions, UVPD produces predominantly a/b-type ions with greatly reduced abundances of y ions. Immonium ions, mostly ones from aromatic or basic amino acids, are also observed in the low m/z range upon UVPD. UVPD of peptides containing two chromophore moieties (with one at the C-terminus and another at an acidic residue) results in even more efficient photodissociation at the expense of the annihilation of almost all diagnostic b and y ions containing the chromophore.
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Affiliation(s)
- Byoung Joon Ko
- Department of Chemical Engineering, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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92
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93
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McLuckey SA, Mentinova M. Ion/neutral, ion/electron, ion/photon, and ion/ion interactions in tandem mass spectrometry: do we need them all? Are they enough? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:3-12. [PMID: 21472539 PMCID: PMC3240857 DOI: 10.1007/s13361-010-0004-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 09/06/2010] [Accepted: 09/13/2010] [Indexed: 05/04/2023]
Abstract
A range of strategies and tools have been developed to facilitate the determination of primary structures of analyte molecules of interest via tandem mass spectrometry (MS/MS). The two main factors that determine the primary structural information present in an MS/MS spectrum are the type of ion generated from the analyte molecule and the dissociation method. The ion type subjected to dissociation is determined by the ionization method/conditions and ion transformation processes that might take place after initial gas-phase ion formation. Furthermore, the range of analyte-related ion types can be expanded via derivatization reactions prior to mass spectrometry. Dissociation methods include those that simply alter the population of internal states of the mass-selected ion (i.e., activation methods like collision-induced dissociation) as well as processes that rely on the transformation of the ion type prior to dissociation (e.g., electron capture dissociation). A variety of ion interactions have been studied for the purpose of ion dissociation and ion transformation, including ion/neutral, ion/photon, ion/electron, and ion/ion interactions. A wide range of phenomena have been observed, many of which have been explored/developed as means for structural analysis. The techniques arising from these phenomena are discussed within the context of the elements of structural determination in tandem mass spectrometry: ion-type definition and dissociation. Unique aspects of the various ion interactions are emphasized along with any barriers to widespread implementation.
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Affiliation(s)
- Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA.
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94
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Madsen JA, Boutz DR, Brodbelt JS. Ultrafast ultraviolet photodissociation at 193 nm and its applicability to proteomic workflows. J Proteome Res 2010; 9:4205-14. [PMID: 20578723 DOI: 10.1021/pr100515x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet photodissociation (UVPD) at 193 nm was implemented on a linear ion trap mass spectrometer for high-throughput proteomic workflows. Upon irradiation by a single 5 ns laser pulse, efficient photodissociation of tryptic peptides was achieved with production of a, b, c, x, y, and z sequence ions, in addition to immonium ions and v and w side-chain loss ions. The factors that influence the UVPD mass spectra and subsequent in silico database searching via SEQUEST were evaluated. Peptide sequence aromaticity and the precursor charge state were found to influence photodissociation efficiency more so than the number of amide chromophores, and the ion trap q-value and number of laser pulses significantly affected the number and abundances of diagnostic product ions (e.g., sequence and immonium ions). Also, photoionization background subtraction was shown to dramatically improve SEQUEST results, especially when peptide signals were low. A liquid chromatography-mass spectrometry (LC-MS)/UVPD strategy was implemented and yielded comparable or better results relative to LC-MS/collision induced dissociation (CID) for analysis of proteolyzed bovine serum albumin and lysed human HT-1080 cytosolic fibrosarcoma cells.
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Affiliation(s)
- James A Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
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95
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Smith SA, Kalcic CL, Safran KA, Stemmer PM, Dantus M, Reid GE. Enhanced characterization of singly protonated phosphopeptide ions by femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fs-LID-MS/MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:2031-2040. [PMID: 20888783 DOI: 10.1016/j.jasms.2010.08.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 08/22/2010] [Accepted: 08/23/2010] [Indexed: 05/29/2023]
Abstract
To develop an improved understanding of the regulatory role that post-translational modifications (PTMs) involving phosphorylation play in the maintenance of normal cellular function, tandem mass spectrometry (MS/MS) strategies coupled with ion activation techniques such as collision-induced dissociation (CID) and electron-transfer dissociation (ETD) are typically employed to identify the presence and site-specific locations of the phosphate moieties within a given phosphoprotein of interest. However, the ability of these techniques to obtain sufficient structural information for unambiguous phosphopeptide identification and characterization is highly dependent on the ion activation method employed and the properties of the precursor ion that is subjected to dissociation. Herein, we describe the application of a recently developed alternative ion activation technique for phosphopeptide analysis, termed femtosecond laser-induced ionization/dissociation (fs-LID). In contrast to CID and ETD, fs-LID is shown to be particularly suited to the analysis of singly protonated phosphopeptide ions, yielding a wide range of product ions including a, b, c, x, y, and z sequence ions, as well as ions that are potentially diagnostic of the positions of phosphorylation (e.g., 'a(n)+1-98'). Importantly, the lack of phosphate moiety losses or phosphate group 'scrambling' provides unambiguous information for sequence identification and phosphorylation site characterization. Therefore, fs-LID-MS/MS can serve as a complementary technique to established methodologies for phosphoproteomic analysis.
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Affiliation(s)
- Scott A Smith
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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96
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Vasicek L, Brodbelt JS. Enhancement of ultraviolet photodissociation efficiencies through attachment of aromatic chromophores. Anal Chem 2010; 82:9441-6. [PMID: 20961088 DOI: 10.1021/ac102126s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two N-terminal derivatization reagents containing aromatic chromophores, 4-sulfophenyl isothiocyanate (SPITC) and 4-methylphosphonophenyl isothiocyanate (PPITC), were used to increase the dissociation efficiencies of peptides upon ultraviolet photodissociation (UVPD) at 193 nm. The resulting UVPD spectra are dominated by C-terminal ions, including y, z, x, v, and w ions, and immonium ions. The attachment of the PPITC or SPITC groups leads to a reduction in the number and abundances of N-terminal ions because the added phosphonate or sulfonate functionalities result in neutralization of some of the N-terminal species, ones that might normally be singly protonated in the absence of the negatively charged sulfonate or phosphonate groups. In addition, the greater photoabsorptivities of the PPITC- and SPITC-derivatized N-terminal product ions enhanced their secondary photodissociation, leading to formation of immonium ions.
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Affiliation(s)
- Lisa Vasicek
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
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97
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Hong ES, Yoon HJ, Kim B, Yim YH, So HY, Shin SK. Mass spectrometric studies of alkali metal ion binding on thrombin-binding aptamer DNA. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1245-1255. [PMID: 20434362 DOI: 10.1016/j.jasms.2010.03.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 03/09/2010] [Accepted: 03/10/2010] [Indexed: 05/29/2023]
Abstract
The binding sites and consecutive binding constants of alkali metal ions, (M(+) = Na(+), K(+), Rb(+), and Cs(+)), to thrombin-binding aptamer (TBA) DNA were studied by Fourier-transform ion cyclotron resonance spectrometry. TBA-metal complexes were produced by electrospray ionization (ESI) and the ions of interest were mass-selected for further characterization. The structural motif of TBA in an ESI solution was checked by circular dichroism. The metal-binding constants and sites were determined by the titration method and infrared multiphoton dissociation (IRMPD), respectively. The binding constant of potassium is 5-8 times greater than those of other alkali metal ions, and the potassium binding site is different from other metal binding sites. In the 1:1 TBA-metal complex, potassium is coordinated between the bottom G-quartet and two adjacent TT loops of TBA. In the 1:2 TBA-metal complex, the second potassium ion binds at the TGT loop of TBA, which is in line with the antiparallel G-quadruplex structure of TBA. On the other hand, other alkali metal ions bind at the lateral TGT loop in both 1:1 and 1:2 complexes, presumably due to the formation of ion-pair adducts. IRMPD studies of the binding sites in combination with measurements of the consecutive binding constants help elucidate the binding modes of alkali metal ions on DNA aptamer at the molecular level.
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Affiliation(s)
- Eun Sun Hong
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
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98
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Chingin K, Frankevich V, Balabin R, Barylyuk K, Chen H, Wang R, Zenobi R. Direct Access to Isolated Biomolecules under Ambient Conditions. Angew Chem Int Ed Engl 2010; 49:2358-61. [DOI: 10.1002/anie.200906213] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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99
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Chingin K, Frankevich V, Balabin R, Barylyuk K, Chen H, Wang R, Zenobi R. Direct Access to Isolated Biomolecules under Ambient Conditions. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906213] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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100
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Vasicek L, Brodbelt JS. Enhanced electron transfer dissociation through fixed charge derivatization of cysteines. Anal Chem 2009; 81:7876-84. [PMID: 19722535 DOI: 10.1021/ac901482s] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron transfer dissociation (ETD) has proven to be a promising new ion activation method for proteomics applications due to its ability to generate c- and z-type fragment ions in comparison to the y- and b-type ions produced upon the more conventional collisional activation of peptides. However, low precursor charge states hinder the success of electron-based activation methods due to competition from nondissociative charge reduction and incomplete sequence coverage. In the present report, the reduction and alkylation of disulfide bonds prior to ETD analysis is evaluated by comparison of three derivatization reagents: iodoacetamide (IAM), N,N-dimethyl-2-chloro-ethylamine (DML), and (3-acrylamidopropyl)-trimethyl ammonium chloride (APTA). While both the DML and APTA modifications lead to an increase in the charge states of peptides, the APTA-peptides provided the most significant improvement in percent fragmentation and sequence coverage for all peptides upon ETD, including formation of diagnostic ions that allow characterization of both the C- and N-termini. In addition, the formation of product ions in multiple charge states upon ETD is minimized for the APTA-modified peptides.
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Affiliation(s)
- Lisa Vasicek
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
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