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Khreis JM, Reitshammer J, Vizcaino V, Klawitter K, Feketeová L, Denifl S. High-energy collision-induced dissociation of histidine ions [His + H] + and [His - H] - and histidine dimer [His 2 + H] . RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:113-120. [PMID: 29108138 DOI: 10.1002/rcm.8027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/05/2017] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Histidine (His) is an essential amino acid, whose side group consists of an aromatic imidazole moiety that can bind a proton or metal cation and act as a donor in intermolecular interactions in many biological processes. While the dissociation of His monomer ions is well known, information on the kinetic energy released in the dissociation is missing. METHODS Using a new home-built electrospray ionization (ESI) source adapted to a double-focusing mass spectrometer of BE geometry, we investigated the fragmentation reactions of protonated and deprotonated His, [His + H]+ and [His - H]- , and the protonated His dimer [His2 + H]+ , accelerated to 6 keV in a high-energy collision with helium gas. We evaluated the kinetic energy release (KER) for the observed dissociation channels. RESULTS ESI of His solution in positive mode led to the formation of His clusters [Hisn + H]+ , n = 1-6, with notably enhanced stability of the tetramer. [His + H]+ dissociates predominantly by loss of (H2 O + CO) with a KER of 278 meV, while the dominant dissociation channel of [His - H]- involves loss of NH3 with a high KER of 769 meV. Dissociation of [His2 + H]+ is dominated by loss of the monomer but smaller losses are also observed. CONCLUSIONS The KER for HCOOH loss from both [His + H]+ and [His - H]- is similar at 278 and 249 meV, respectively, which suggests that the collision-induced dissociation takes place via a similar mechanism. The loss of COOH and C2 H5 NO2 from the dimer suggests that the dimer of His binds through a shared proton between the imidazole moieties.
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Affiliation(s)
- Jusuf M Khreis
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Julia Reitshammer
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | | | - Kevin Klawitter
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Linda Feketeová
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
- Université de Lyon, Université Claude Bernard Lyon1, CNRS/IN2P3, UMR5822, Institut de Physique Nucléaire de Lyon, 43 Bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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Jacobs AD, Jovan Jose KV, Horness R, Raghavachari K, Thielges MC, Clemmer DE. Cooperative Formation of Icosahedral Proline Clusters from Dimers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:95-102. [PMID: 29127569 PMCID: PMC6884317 DOI: 10.1007/s13361-017-1833-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/28/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
Ion mobility spectrometry-mass spectrometry and Fourier transform infrared spectroscopy (FTIR) techniques were combined with quantum chemical calculations to examine the origin of icosahedral clusters of the amino acid proline. When enantiopure proline solutions are electrosprayed (using nanospray) from 100 mM ammonium acetate, only three peaks are observed in the mass spectrum across a concentration range of five orders of magnitude: a monomer [Pro+H]+ species, favored from 0.001 to 0.01 mM proline concentrations; a dimer [2Pro+H]+ species, the most abundant species for proline concentrations above 0.01 mM; and, the dimer and dodecamer [12Pro+2H]2+ for 1.0 mM and more concentrated proline solutions. Electrospraying racemic D/L-proline solutions from 100 mM ammonium acetate leads to a monomer at low proline concentrations (0.001 to 0.1 mM), and a dimer at higher concentrations (>0.09 mM), as well as a very small population of 8 to 15 Pro clusters that comprise <0.1% of the total ion signals even at the highest proline concentration. Solution FTIR studies show unique features that increase in intensity in the enantiopure proline solutions, consistent with clustering, presumably from the icosahedral geometry in bulk solution. When normalized for the total proline, these results are indicative of a cooperative formation of the enantiopure 12Pro species from 2Pro. Graphical Abstract.
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Affiliation(s)
- Alexander D Jacobs
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - K V Jovan Jose
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Rachel Horness
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | | | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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3
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Seo J, Warnke S, Pagel K, Bowers MT, von Helden G. Infrared spectrum and structure of the homochiral serine octamer–dichloride complex. Nat Chem 2017; 9:1263-1268. [DOI: 10.1038/nchem.2821] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 06/06/2017] [Indexed: 01/14/2023]
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Bleiholder C, Bowers MT. The Solution Assembly of Biological Molecules Using Ion Mobility Methods: From Amino Acids to Amyloid β-Protein. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:365-386. [PMID: 28375705 PMCID: PMC6287953 DOI: 10.1146/annurev-anchem-071114-040304] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) methods are increasingly used to study noncovalent assemblies of peptides and proteins. This review focuses on the noncovalent self-assembly of amino acids and peptides, systems at the heart of the amyloid process that play a central role in a number of devastating diseases. Three different systems are discussed in detail: the 42-residue peptide amyloid-β42 implicated in the etiology of Alzheimer's disease, several amyloid-forming peptides with 6-11 residues, and the assembly of individual amino acids. We also discuss from a more fundamental perspective the processes that determine how quickly proteins and their assemblies denature when the analyte ion has been stripped of its solvent in an IMS-MS measurement and how to soften the measurement so that biologically meaningful data can be recorded.
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Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306;
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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Singh P, Brar SK, Bajaj M, Narang N, Mithu VS, Katare OP, Wangoo N, Sharma RK. Self-assembly of aromatic α-amino acids into amyloid inspired nano/micro scaled architects. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 72:590-600. [DOI: 10.1016/j.msec.2016.11.117] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/12/2016] [Accepted: 11/26/2016] [Indexed: 01/01/2023]
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Do TD, de Almeida NEC, LaPointe NE, Chamas A, Feinstein SC, Bowers MT. Amino Acid Metaclusters: Implications of Growth Trends on Peptide Self-Assembly and Structure. Anal Chem 2015; 88:868-76. [PMID: 26632663 DOI: 10.1021/acs.analchem.5b03454] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion-mobility mass spectrometry is utilized to examine the metacluster formation of serine, asparagine, isoleucine, and tryptophan. These amino acids are representative of different classes of noncharged amino acids. We show that they can form relatively large metaclusters in solution that are difficult or impossible to observe by traditional solution techniques. We further demonstrate, as an example, that the formation of Ser metaclusters is not an ESI artifact because large metaclusters can be detected in negative polarity and low concentration with similar cross sections to those measured in positive polarity and higher concentration. The growth trends of tryptophan and isoleucine metaclusters, along with serine, asparagine, and the previously studied phenylalanine, are balanced among various intrinsic properties of individual amino acids (e.g., hydrophobicity, size, and shape). The metacluster cross sections of hydrophilic residues (Ser, Asn, Trp) tend to stay on or fall below the isotropic model trend lines whereas those of hydrophobic amino acids (Ile, Phe) deviate positively from the isotropic trend lines. The growth trends correlate well to the predicted aggregation propensity of individual amino acids. From the metacluster data, we introduce a novel approach to score and predict aggregation propensity of peptides, which can offer a significant improvement over the existing methods in terms of accuracy. Using a set of hexapeptides, we show that the strong negative deviations of Ser metaclusters from the isotropic model leads a prediction of microcrystalline formation for the SFSFSF peptide, whereas the strong positive deviation of Ile leads to prediction or fibril formation for the NININI peptide. Both predictions are confirmed experimentally using ion mobility and TEM measurements. The peptide SISISI is predicted to only weakly aggregate, a prediction confirmed by TEM.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Natália E C de Almeida
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Nichole E LaPointe
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Ali Chamas
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Stuart C Feinstein
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
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7
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Feketeová L, Khairallah GN, O'Hair RAJ, Nielsen SB. Gas-phase fragmentation of deprotonated tryptophan and its clusters [Trpn -H]- induced by different activation methods. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1395-1402. [PMID: 26147479 DOI: 10.1002/rcm.7233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/19/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
RATIONALE Non-covalent amino acid clusters are the subject of intense research in diverse areas including peptide bond formation studies or the determination of proton affinities or methylating abilities of amino acids. However, most of the research has focused on positive ions and little is known about anionic clusters. METHODS Fragmentation reactions of deprotonated tryptophan (Trp), [Trp-H](-) and Trp singly deprotonated non-covalently bound clusters [Trp(n) -H](-), n = 2, 3, 4, were investigated using low-energy collision-induced dissociation (CID) with He atoms, high-energy CID with Na atoms, and electron-induced dissociation (EID) with 20-35 eV electrons. Fragmentation of the monomeric Trp anion, where all labile hydrogens were exchanged for deuterium [d(4) -Trp-D](-), was investigated using low-energy CID and EID, in order to shed light on the dissociation mechanisms. RESULTS The main fragmentation channel for Trp cluster anions, [Trp(n) -H](-), n >1, is the loss of the neutral monomer. The fragmentation of the deprotonated Trp monomer induced by electrons resembles the fragmentation induced by high-energy collisions through electronic excitation of the parent. However, the excitation must precede in a different way, shown through only monomer loss from larger clusters, n >1, in case of EID, but intracluster chemistry in the case of high-energy CID. CONCLUSIONS The anion of the indole ring C(8)H(6) N(-) has been identified in the product ion spectra of [Trp(n) -H](-) using all activation methods, thus providing a diagnostic marker ion. No evidence was found for formation of peptide bonds as a route to prebiotic peptides in the fragmentation reactions of these singly deprotonated Trp cluster ions.
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Affiliation(s)
- Linda Feketeová
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
- Université de Lyon, 69003 Lyon, France; Université Claude Bernard Lyon1; Institut de Physique Nucléaire de Lyon, CNRS/IN2P3, UMR5822, 69622 Villeurbanne, France
| | - George N Khairallah
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Richard A J O'Hair
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Steen Brøndsted Nielsen
- Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, Aarhus C, 8000, Denmark
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8
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Greer SM, Parker WR, Brodbelt JS. Impact of Protease on Ultraviolet Photodissociation Mass Spectrometry for Bottom-up Proteomics. J Proteome Res 2015; 14:2626-32. [DOI: 10.1021/acs.jproteome.5b00165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| | - W. Ryan Parker
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
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9
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Atlasevich N, Holliday AE, Valentine SJ, Clemmer DE. Collisional activation of [14Pro+2H]2+ clusters: chiral dependence of evaporation and fission processes. J Phys Chem B 2012; 116:7644-51. [PMID: 22668003 PMCID: PMC3503484 DOI: 10.1021/jp303778w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ion mobility/mass spectrometry techniques are used to investigate the dissociation of the small proline cluster [14Pro+2H](2+) produced by electrospray ionization. While this cluster is known to prefer heterochiral compositions (i.e., mixed L- and D-compositions, J. Phys. Chem. A, submitted for publication), it is possible to produce homochiral forms by electrospraying solutions containing only L- or D-proline. Differences in the measured cross sections for [14Pro+2H](2+) produced from enantiomerically pure (100% l or 100% d) or racemic (50:50 l/d) solutions indicate that homochiral and heterochiral clusters have different structures. Upon low-energy collisional activation, both the heterochiral and homochiral doubly charged structures evaporate neutral proline monomers, resulting in the formation of [xPro+2H](2+) ions (where x = 9-13). At higher activation energies, there is evidence that these smaller clusters (primarily [10Pro+2H](2+)) fission to produce [xPro+H](+) (where x = 1-6). Analysis of product ion intensities reveals a strong chiral preference associated with fissioning. Products of evaporation also show a chiral dependence but to a lesser extent.
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Affiliation(s)
| | - Alison E. Holliday
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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Kalli A, Hess S. Fragmentation of singly, doubly, and triply charged hydrogen deficient peptide radical cations in infrared multiphoton dissociation and electron induced dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:244-263. [PMID: 22101468 DOI: 10.1007/s13361-011-0272-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 05/31/2023]
Abstract
Gas phase fragmentation of hydrogen deficient peptide radical cations continues to be an active area of research. While collision induced dissociation (CID) of singly charged species is widely examined, dissociation channels of singly and multiply charged radical cations in infrared multiphoton dissociation (IRMPD) and electron induced dissociation (EID) have not been, so far, investigated. Here, we report on the gas phase dissociation of singly, doubly and triply charged hydrogen deficient peptide radicals, [M + nH]((n+1)+·) (n=0, 1, 2), in MS(3) IRMPD and EID and compare the observed fragmentation pathways to those obtained in MS(3) CID. Backbone fragmentation in MS(3) IRMPD and EID was highly dependent on the charge state of the radical precursor ions, whereas amino acid side chain cleavages were largely independent of the charge state selected for fragmentation. Cleavages at aromatic amino acids, either through side chain loss or backbone fragmentation, were significantly enhanced over other dissociation channels. For singly charged species, the MS(3) IRMPD and EID spectra were mainly governed by radical-driven dissociation. Fragmentation of doubly and triply charged radical cations proceeded through both radical- and charge-driven processes, resulting in the formation of a wide range of backbone product ions including, a-, b-, c-, y-, x-, and z-type. While similarities existed between MS(3) CID, IRMPD, and EID of the same species, several backbone product ions and side chain losses were unique for each activation method. Furthermore, dominant dissociation pathways in each spectrum were dependent on ion activation method, amino acid composition, and charge state selected for fragmentation.
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Affiliation(s)
- Anastasia Kalli
- Proteome Exploration Laboratory, Division of Biology, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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Kalli A, Grigorean G, Håkansson K. Electron induced dissociation of singly deprotonated peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2209-2221. [PMID: 21952776 DOI: 10.1007/s13361-011-0233-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/11/2011] [Accepted: 08/12/2011] [Indexed: 05/31/2023]
Abstract
Dissociation of singly charged species is more challenging compared with that of multiply charged precursor ions because singly charged ions are generally more stable. In collision activated dissociation (CAD), singly charged ions also gain less kinetic energy in a fixed electric field compared with multiply charged species. Furthermore, ion-electron and ion-ion reactions that frequently provide complementary and more extensive fragmentation compared with CAD typically require multiply charged precursor ions. Here, we investigate electron induced dissociation (EID) of singly deprotonated peptides and compare the EID fragmentation patterns with those observed in negative ion mode CAD. Fragmentation induced upon electron irradiation and collisional activation is not specific and results in the formation of a wide range of product ions, including b-, y-, a-, x-, c-, and z-type ions. Characteristic amino acid side chain losses are detected in both techniques. However, differences are also observed between EID and CAD spectra of the same species, including formation of odd-electron species not seen in CAD, in EID. Furthermore, EID frequently results in more extensive fragmentation compared with CAD. For modified peptides, EID resulted in retention of sulfonation and phosphorylation, allowing localization of the modification site. The observed differences are likely due to both vibrational and electronic excitation in EID, whereas only the former process occurs in CAD.
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Affiliation(s)
- Anastasia Kalli
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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Kong X. Serine-phosphoric acid cluster ions studied by electrospray ionization and tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:535-545. [PMID: 21630381 DOI: 10.1002/jms.1922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
More than 310 kinds of cluster ions of S(m) P(n) H(k) (k+) are observed in a single ESI mass spectrum of a mixed solution of serine and phosphoric acid. Some typical cluster ions are selected, activated by collision in a FT ICR cell, and the dissociation pathways were deduced in detail. For large singly protonated ions, the collisions cause the ejection of subunits of serine or phosphoric acid subsequently producing the ions of S(2) P(4) H(1) (1+) , which can be further dissociated by the loss of phosphoric acid molecules in turn and form the protonated serine dimer and monomer. However, for the doubly protonated ions, the dissociation pathways change from the loss of a protonated serine dimer for the ions of S(7) P(9) H(2) (2+) to the neutral loss of H(3) PO(4) for the ions of S(7) P(12) H(2) (2+) or the neutral loss of serine or H(3) PO(4) for the larger clusters, indicating the effect of cluster sizes on the process of dissociation. The structure of S(2) P(4) H(1) (1+) is suggested based on B3LYP/6-31G(d,p) calculations. The diversity and structural orderliness of the hetero-cluster ions are mainly attributed to the network of hydrogen bonds inside the cluster ions and the extraordinary amphotericity of the components.
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Affiliation(s)
- Xianglei Kong
- The State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China.
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