1
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Giraud R, Le Blanc YJC, Guna M, Hopfgartner G. Ultraviolet photodissociation and collision-induced dissociation for qualitative/quantitative analysis of low molecular weight compounds by liquid chromatography-mass spectrometry. Anal Bioanal Chem 2023; 415:7117-7126. [PMID: 37803134 PMCID: PMC10684635 DOI: 10.1007/s00216-023-04977-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
Collision-induced dissociation (CID) is the most wildly used fragmentation technique for qualitative and quantitative determination of low molecular weight compounds (LMWC). Ultraviolet photodissociation (UVPD) has been mainly investigated for the analysis of peptides and lipids while only in a limited way for LMWC. A triple quadrupole linear ion trap instrument has been modified to allow ultraviolet photodissociation (UVPD) in the end of the q2 region enabling various workflows with and without data-dependent acquisition (DDA) combining CID and UVPD in the same LC-MS analysis. The performance of UVPD, with a 266-nm laser, is compared to CID for a mix of 90 molecules from different classes of LMWC including peptides, pesticides, pharmaceuticals, metabolites, and drugs of abuse. These two activation methods offer complementary fragments as well as common fragments with similar sensitivities for most analytes investigated. The versatility of UVPD and CID is also demonstrated for quantitative analysis in human plasma of bosentan and its desmethyl metabolite, used as model analytes. Different background signals are observed for both fragmentation methods as well as unique fragments which opens the possibility of developing a selective quantitative assay with improved sample throughput, in particular for analytes present in different matrices.
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Affiliation(s)
- Romain Giraud
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1205, Geneva 4, Switzerland
| | | | | | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1205, Geneva 4, Switzerland.
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2
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Sasiene ZJ, Mendis PM, Jackson GP. Quantitative Assessment of Six Different Reagent Gases for Charge Transfer Dissociation (CTD) of Biological Ions. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 462:116532. [PMID: 33679212 PMCID: PMC7928426 DOI: 10.1016/j.ijms.2021.116532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Charge transfer dissociation mass spectrometry (CTD-MS) has been shown to induce high energy fragmentation of biological ions in the gas phase and provide fragmentation spectra similar to extreme ultraviolet photodissociation (XUVPD). To date, CTD has typically employed helium cations with kinetic energies between 4-10 keV to initiate radical-directed fragmentation of analytes. However, as a reagent, helium has recently been listed as a critical mineral that is becoming scarcer and more expensive, so this study explored the potential for using cheaper and more readily available reagent gases. A model peptide, bradykinin, and a model oligosaccharide, κ-carrageenan with a degree of polymerization of 4, were fragmented using a variety of CTD reagent gases, which included helium, hydrogen, oxygen, nitrogen, argon and lab air. The CTD results were also contrasted with low-energy collision-induced dissociation (LE-CID), which were collected on the same 3D ion trap. Using constant reagent ion fluxes and kinetic energies, all five alterative reagent gases generated remarkably consistent sequence coverage and fragmentation efficiencies relative to He-CTD, which suggests that the ionization energy of the reagent gas has a negligible effect on the activation of the biological ions. The CTD efficiencies of all the gases ranged from 11-13% for bradykinin and 7-8% for κ-carrageenan. Within these tight ranges, the abundance of the CTnoD peak of bradykinin and the efficiency of CTD fragmentation of bradykinin both correlated with the ionization energy of the CTD reagent gas, which suggests that resonant charge transfer plays a small role in the activation of this peptide. The majority of the excitation energy for bradykinin and for κ-carrageenan comes from an electron stopping mechanism, which is described by long-range interactions between the reagent cations and electrons in the highest occupied molecular orbitals (HOMOs) of the biological ions. The CTD spectra do not provide any evidence for covalently bound products between the biological ions and the more-reactive gases like hydrogen, oxygen and nitrogen, which implies that the high kinetic energies of the reagent ions make them unavailable for covalent reactions. This work demonstrates that any of the substitute reagent gases tested are viable options for future CTD-MS experiments.
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Affiliation(s)
- Zachary J. Sasiene
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506-6121, USA
| | - Praneeth M. Mendis
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506-6121, USA
| | - Glen P. Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506-6121, USA
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV 26506-6121, USA
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3
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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4
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Solovyeva EM, Kopysov VN, Pereverzev AY, Lobas AA, Moshkovskii SA, Gorshkov MV, Boyarkin OV. Method for Identification of Threonine Isoforms in Peptides by Ultraviolet Photofragmentation of Cold Ions. Anal Chem 2019; 91:6709-6715. [DOI: 10.1021/acs.analchem.9b00770] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elizaveta M. Solovyeva
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld.2 Moscow, 119334, Russia
| | - Vladimir N. Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Anna A. Lobas
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld.2 Moscow, 119334, Russia
| | | | - Mikhail V. Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld.2 Moscow, 119334, Russia
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
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5
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Dilillo M, de Graaf EL, Yadav A, Belov ME, McDonnell LA. Ultraviolet Photodissociation of ESI- and MALDI-Generated Protein Ions on a Q-Exactive Mass Spectrometer. J Proteome Res 2018; 18:557-564. [PMID: 30484663 DOI: 10.1021/acs.jproteome.8b00896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The identification of molecular ions produced by MALDI or ESI strongly relies on their fragmentation to structurally informative fragments. The widely diffused fragmentation techniques for ESI multiply charged ions are either incompatible (ECD and ETD) or show lower efficiency (CID, HCD), with the predominantly singly charged peptide and protein ions formed by MALDI. In-source decay has been successfully adopted to sequence MALDI-generated ions, but it further increases spectral complexity, and it is not compatible with mass-spectrometry imaging. Excellent UVPD performances, in terms of number of fragment ions and sequence coverage, has been demonstrated for electrospray ionization for multiple proteomics applications. UVPD showed a much lower charge-state dependence, and so protein ions produced by MALDI may exhibit equal propensity to fragment. Here we report UVPD implementation on an Orbitrap Q-Exactive Plus mass spectrometer equipped with an ESI/EP-MALDI. UVPD of MALDI-generated ions was benchmarked against MALDI-ISD, MALDI-HCD, and ESI-UVPD. MALDI-UVPD outperformed MALDI-HCD and ISD, efficiently sequencing small proteins ions. Moreover, the singly charged nature of MALDI-UVPD avoids the bioinformatics challenges associated with highly congested ESI-UVPD mass spectra. Our results demonstrate the ability of UVPD to further improve tandem mass spectrometry capabilities for MALDI-generated protein ions. Data are available via ProteomeXchange with identifier PXD011526.
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Affiliation(s)
- Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy
| | - Erik L de Graaf
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy
| | - Avinash Yadav
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy.,Scuola Normale Superiore di Pisa , 56126 Pisa , Italy
| | - Mikhail E Belov
- Spectroglyph LLC , Kennewick , Washington 99338 , United States
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy.,Center for Proteomics and Metabolomics , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
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6
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Holden DD, Sanders JD, Weisbrod CR, Mullen C, Schwartz JC, Brodbelt JS. Implementation of Fragment Ion Protection (FIP) during Ultraviolet Photodissociation (UVPD) Mass Spectrometry. Anal Chem 2018; 90:8583-8591. [PMID: 29927232 DOI: 10.1021/acs.analchem.8b01723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ultraviolet photodissociation (UVPD) is a nonselective activation method in which both precursor and fragment ions may absorb photons and dissociate. Photoactivation of fragment ions may result in secondary or multiple generations of dissociation, which decreases the signal-to-noise ratio (S/N) of larger fragment ions owing to the prevalent subdivision of the ion current into many smaller, often less informative, fragment ions. Here we report the use of dipolar excitation waveforms to displace fragment ions out of the laser beam path, thus alleviating the extent of secondary dissociation during 193 nm UVPD. This fragment ion protection (FIP) strategy increases S/N of larger fragment ions and improves the sequence coverage obtained for proteins via retaining information deeper into the midsection of protein sequences.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - James D Sanders
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Chad R Weisbrod
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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7
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Jayasekharan T, Gupta SL, Dhiman V. Binding of Cu + and Cu 2+ with peptides: Peptides = oxytocin, Arg 8 -vasopressin, bradykinin, angiotensin-I, substance-P, somatostatin, and neurotensin. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:296-313. [PMID: 29333632 DOI: 10.1002/jms.4062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
The intrinsic binding ability of 7 natural peptides (oxytocin, arg8 -vasopressin, bradykinin, angiotensin-I, substance-P, somatostatin, and neurotensin) with copper in 2 different oxidation states (CuI/II ) derived from different Cu+/2+ precursor sources have been investigated for their charge-dependent binding characteristics. The peptide-CuI/II complexes, [M - (n-1)H + nCuI ] and [M - (2n-1)H + nCuII ], are prepared/generated by the reaction of peptides with CuI solution/Cu-target and CuSO4 solution and are analyzed by using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. The MALDI mass spectra of both [M - (n-1)H + nCuI ] and [M - (2n-1)H + nCuII ] complexes show no mass shift due to the loss of ─H atoms in the main chain ─NH of these peptides by Cu+ and Cu2+ deprotonation. The measured m/z value indicates the reduction of CuI/II oxidation state into Cu0 during MALDI processes. The number and relative abundance of Cu+ bound to the peptides are greater compared with the Cu2+ bound peptides. Oxytocin, arg8 -vasopressin, bradykinin, substance-P, and somatostatin show the binding of 5Cu+ , and angiotensin-I and neurotensin show the binding of 7Cu+ from both CuI and Cu targets, while bradykinin shows the binding of 2Cu2+ , oxytocin, arg8 -vasopressin, angiotensin-I, and substance-P; somatostatin shows the binding of 3Cu2+ ; and neurotensin shows 4Cu2+ binding. The binding of more Cu+ with these small peptides signifies that the bonding characteristics of both Cu+ and Cu2+ are different. The amino acid residues responsible for the binding of both Cu+ and Cu2+ in these peptides have been identified based on the density functional theory computed binding energy values of Cu+ and the fragment transformation method predicted binding preference of Cu2+ for individual amino acids.
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Affiliation(s)
- Thankan Jayasekharan
- Atomic and Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Shyam L Gupta
- Atomic and Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Vikas Dhiman
- Atomic and Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
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8
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Holden DD, Brodbelt JS. Improving Performance Metrics of Ultraviolet Photodissociation Mass Spectrometry by Selective Precursor Ejection. Anal Chem 2016; 89:837-846. [PMID: 28105830 DOI: 10.1021/acs.analchem.6b03777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods. The lower S/N is attributed to the dispersion of ion current among numerous fragment ion channels (a,b,c,x,y,z ions). In addition, frequently UVPD is performed such that a relatively large population of precursor ions remains undissociated after the UV photoactivation period in order to prevent overdissociation into small uninformative or internal fragment ions. Here we report a method to improve spectral S/N and increase the accuracy of mass assignments of UVPD mass spectra via resonance ejection of undissociated precursor ions after photoactivation. This strategy, termed precursor ejection UVPD or PE-UVPD, allows the ion trap to be filled with more ions prior to UVPD while at the same time alleviating the space charge problems that would otherwise contribute to the skewing of mass assignments and reduction of S/N. Here we report the performance gains by implementation of PE-UVPD for peptide analysis in an ion trap mass spectrometer.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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9
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light‐Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dustin D. Holden
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH Hanna-Kunath-Strasse 11 28199 Bremen Germany
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - James D. Sanders
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - Jennifer S. Brodbelt
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
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10
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light-Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016; 55:12417-21. [PMID: 27605434 DOI: 10.1002/anie.201605850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/02/2016] [Indexed: 11/09/2022]
Abstract
The first application of light-emitting diodes (LEDs) for ultraviolet photodissociation (UVPD) mass spectrometry is reported. LEDs provide a compact, low cost light source and have been incorporated directly into the trapping cell of an Orbitrap mass spectrometer. MS/MS efficiencies of over 50 % were obtained using an extended irradiation period, and UVPD was optimized by modulating the ion trapping parameters to maximize the overlap between the ion cloud and the irradiation volume.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199, Bremen, Germany
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA.
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11
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Shaw JB, Robinson EW, Paša-Tolić L. Vacuum Ultraviolet Photodissociation and Fourier Transform–Ion Cyclotron Resonance (FT-ICR) Mass Spectrometry: Revisited. Anal Chem 2016; 88:3019-23. [DOI: 10.1021/acs.analchem.6b00148] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jared B. Shaw
- Environmental Molecular Sciences
Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Errol W. Robinson
- Environmental Molecular Sciences
Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences
Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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12
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Moon JH, Yoon S, Bae YJ, Kim MS. Formation of gas-phase peptide ions and their dissociation in MALDI: insights from kinetic and ion yield studies. MASS SPECTROMETRY REVIEWS 2015; 34:94-115. [PMID: 24863621 DOI: 10.1002/mas.21427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/17/2014] [Indexed: 06/03/2023]
Abstract
Insights on mechanisms for the generation of gas-phase peptide ions and their dissociation in matrix-assisted laser desorption ionization (MALDI) gained from the kinetic and ion yield studies are presented. Even though the time-resolved photodissociation technique was initially used to determine the dissociation kinetics of peptide ions and their effective temperature, it was replaced by a simpler method utilizing dissociation yields from in-source decay (ISD) and post-source decay (PSD). The ion yields for a matrix and a peptide were measured by repeatedly irradiating a region on a sample and collecting ion signals until the sample in the region was completely depleted. Matrix- and peptide-derived gas-phase cations were found to be generated by pre-formed ion emission or by ion-pair emission followed by anion loss, but not by laser-induced ionization. The total number of ions, that is, matrix plus peptide, was found to be equal to the number of ions emitted from a pure matrix. A matrix plume was found to cool as it expanded, from around 800-1,000 K to 400-500 K. Dissociation of peptide ions along b/y channels was found to occur statistically, that is, following RRKM behavior. Small critical energy (E0 = 0.6-0.7 eV) and highly negative critical entropy (ΔS(‡) = -30 to -25 eu) suggested that the transition structure was stabilized by multiple intramolecular interactions.
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Affiliation(s)
- Jeong Hee Moon
- Medical Proteomics Research Center, KRIBB, Daejeon, 305-806, Korea
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13
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Ko BJ, Brodbelt JS. Comparison of Glycopeptide Fragmentation by Collision Induced Dissociation and Ultraviolet Photodissociation. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 377:385-392. [PMID: 25844059 PMCID: PMC4379704 DOI: 10.1016/j.ijms.2014.07.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A comparison of the fragmentation pathways of both protonated and deprotonated O-linked glycopeptides from fetuin and κ-casein obtained upon collision induced dissociation (CID) and 193 nm ultraviolet photodissociation (UVPD) in a linear ion trap is presented. A strategy using non-specific pronase digestion, zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) solid phase extraction (SPE) enrichment, and nano-liquid chromatography (nano-LC) is employed. UVPD of deprotonated glycopeptides generally produced the greatest array of fragment ions, thus affording the most diagnostic information about both glycan structure and peptide sequence. In addition, UVPD generated unique fragment ion such as Y-type ions arising from cleavage at the N-terminus of proline. CID and UVPD of protonated glycopeptides produced fragment ions solely from glycan cleavages.
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Affiliation(s)
- Byoung Joon Ko
- Department of Chemistry, 1 University Station A5300, University of Texas at Austin
| | - Jennifer S Brodbelt
- Department of Chemistry, 1 University Station A5300, University of Texas at Austin
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14
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O'Brien JP, Needham BD, Brown DB, Trent MS, Brodbelt JS. Top-Down Strategies for the Structural Elucidation of Intact Gram-negative Bacterial Endotoxins. Chem Sci 2014; 5:4291-4301. [PMID: 25386333 PMCID: PMC4224326 DOI: 10.1039/c4sc01034e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Re-modelling of lipopolysaccharides, which are the primary constituent of the outer cell membrane of Gram-negative bacteria, modulates pathogenesis and resistance to microbials. Reported herein is the characterization of intact Gram-negative bacterial lipooligosaccharides (LOS) via a new strategy utilizing online liquid chromatography (LC) coupled with ultraviolet photodissociation (UVPD) mass spectrometry. Compared to collision-based MS/MS methods, UVPD and UVPD/HCD promoted a greater array of cleavages within both the glycan and lipid moieties, including C-C, C-N, C-O cleavages in the acyl chains as well as glycosidic and cross-ring cleavages, thus providing the most far-reaching structural characterization of LOS. This LC-MS/MS strategy affords a robust analytical method to structurally characterize complex mixtures of bacterial endotoxins that maintains the integrity of the core oligosaccharide and lipid A domains of LOS, providing direct feedback about the cell envelope architectures and LOS modification strategies involved in resistance host innate immune defense.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
| | - Brittany D Needham
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - Dusty B Brown
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - M Stephen Trent
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
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15
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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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16
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O'Brien JP, Needham BD, Henderson JC, Nowicki EM, Trent MS, Brodbelt JS. 193 nm ultraviolet photodissociation mass spectrometry for the structural elucidation of lipid A compounds in complex mixtures. Anal Chem 2014; 86:2138-45. [PMID: 24446701 PMCID: PMC3958132 DOI: 10.1021/ac403796n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
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Here we implement ultraviolet photodissociation
(UVPD) in an online
liquid chromatographic tandem mass spectrometry (MS/MS) strategy to
support analysis of complex mixtures of lipid A combinatorially modified
during development of vaccine adjuvants. UVPD mass spectrometry at
193 nm was utilized to characterize the structures and fragment ion
types of lipid A from Escherichia coli, Vibrio
cholerae, and Pseudomonas aeruginosa using
an Orbitrap mass spectrometer. The fragment ions generated by UVPD
were compared to those from collision induced dissociation (CID) and
higher energy collision dissociation (HCD) with respect to the precursor
charge state. UVPD afforded the widest array of fragment ion types
including acyl chain C–O, C–N, and C–C bond cleavages
and glycosidic C–O and cross ring cleavages, thus providing
the most comprehensive structural analysis of the lipid A. UVPD exhibited
virtually no dependence on precursor ion charge state and was best
at determining lipid A structure including acyl chain length and composition,
giving it an advantage over collision based methods. UVPD was incorporated
into an LC–MS/MS methodology for the analysis of a number of
structural variants in a complex mixture of combinatorially engineered Escherichia coli lipid A.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States
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17
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O'Brien JP, Brodbelt JS. Structural characterization of gangliosides and glycolipids via ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:10399-407. [PMID: 24083420 DOI: 10.1021/ac402379y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry was used to characterize the structures of amphiphilic glycosphingolipids and gangliosides in comparison to collision induced dissociation (CID) and higher energy collision dissociation (HCD) in a high performance Orbitrap mass spectrometer. UVPD produced the widest array of fragment ions diagnostic for both the ceramide base and oligosaccharide moieties. CID and HCD generated mainly glycosidic B/Y and C/Z cleavages of the oligosaccharides moieties and very few informative fragments related to the hydrophobic ceramide base. Several unique cleavages at the sphingoid base and the fatty acid chain occurred upon UVPD, as well as a wider variety of cross ring cleavages (A/X ions), thus affording differentiation of isobaric gangliosides. An LC-UVPD-MS strategy allowed the elucidation of 27 gangliosides among five different classes.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas, United States 78712
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18
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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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19
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Shaw JB, Li W, Holden DD, Zhang Y, Griep-Raming J, Fellers RT, Early BP, Thomas PM, Kelleher NL, Brodbelt JS. Complete protein characterization using top-down mass spectrometry and ultraviolet photodissociation. J Am Chem Soc 2013; 135:12646-51. [PMID: 23697802 DOI: 10.1021/ja4029654] [Citation(s) in RCA: 266] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The top-down approach to proteomics offers compelling advantages due to the potential to provide complete characterization of protein sequence and post-translational modifications. Here we describe the implementation of 193 nm ultraviolet photodissociation (UVPD) in an Orbitrap mass spectrometer for characterization of intact proteins. Near-complete fragmentation of proteins up to 29 kDa is achieved with UVPD including the unambiguous localization of a single residue mutation and several protein modifications on Pin1 (Q13526), a protein implicated in the development of Alzheimer's disease and in cancer pathogenesis. The 5 ns, high-energy activation afforded by UVPD exhibits far less precursor ion-charge state dependence than conventional collision- and electron-based dissociation methods.
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Affiliation(s)
- Jared B Shaw
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
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20
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Lai CK, Ng DCM, Pang HF, Le Blanc JCY, Hager JW, Fang DC, Cheung ASC, Chu IK. Laser-induced dissociation of singly protonated peptides at 193 and 266 nm within a hybrid linear ion trap mass spectrometer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1119-27. [PMID: 23592116 DOI: 10.1002/rcm.6545] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/08/2013] [Accepted: 02/13/2013] [Indexed: 05/16/2023]
Abstract
RATIONALE We implemented, for the first time, laser-induced dissociation (LID) within a modified hybrid linear ion trap mass spectrometer, QTrap, while preserving the original scanning capabilities and routine performance of the instrument. METHODS Precursor ions of interest were mass-selected in the first quadrupole (Q1), trapped in the radiofrequency-only quadrupole (q2), photodissociated under irradiation with a 193- or 266-nm laser beam in the third quadrupole (q3), and mass-analyzed using the linear ion trap. RESULTS LID of singly charged protonated peptides revealed, in addition to conventional amide-bond cleavages, preferential fragmentation at Cα -C/N-Cα bonds of the backbone as well as at the Cα -Cβ /Cβ -Cγ bonds of the side-chains. The LID spectra of [M+H](+) featured product ions that were very similar to the observed radical-induced fragmentations in the CID spectra of analogous odd-electron radical cations generated through dissociative electron-transfer in metal-ligand-peptide complexes or through laser photolysis of iodopeptides. CONCLUSIONS LID of [M+H](+) ions results in fragmentation channels that are comparable with those observed upon the CID of M(•+) ions, with a range of fascinating radical-induced fragmentations.
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Affiliation(s)
- Cheuk-Kuen Lai
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
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21
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Shaw JB, Madsen JA, Xu H, Brodbelt JS. Systematic comparison of ultraviolet photodissociation and electron transfer dissociation for peptide anion characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1707-15. [PMID: 22895858 PMCID: PMC4460832 DOI: 10.1007/s13361-012-0424-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 05/19/2012] [Accepted: 05/20/2012] [Indexed: 05/10/2023]
Abstract
Ultraviolet photodissociation at 193 nm (UVPD) and negative electron transfer dissociation (NETD) were compared to establish their utility for characterizing acidic proteomes with respect to sequence coverage distributions (a measure of product ion signals across the peptide backbone), sequence coverage percentages, backbone cleavage preferences, and fragmentation differences relative to precursor charge state. UVPD yielded significantly more diagnostic information compared with NETD for lower charge states (n ≤ 2), but both methods were comparable for higher charged species. While UVPD often generated a more heterogeneous array of sequence-specific products (b-, y-, c-, z-, Y-, d-, and w-type ions in addition to a- and x- type ions), NETD usually created simpler sets of a/x-type ions. LC-MS/UVPD and LC-MS/NETD analysis of protein digests utilizing high pH mobile phases coupled with automated database searching via modified versions of the MassMatrix algorithm was undertaken. UVPD generally outperformed NETD in stand-alone searches due to its ability to efficiently sequence both lower and higher charge states with rapid activation times. However, when combined with traditional positive mode CID, both methods yielded complementary information with significantly increased sequence coverage percentages and unique peptide identifications over that of just CID alone.
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Affiliation(s)
- Jared B. Shaw
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
| | - James A. Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
| | - Hua Xu
- Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, BRB 9 Floor, Cleveland, OH, USA 44106
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
- Correspondence to:
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22
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He Y, Parthasarathi R, Raghavachari K, Reilly JP. Photodissociation of charge tagged peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1182-1190. [PMID: 22532332 DOI: 10.1007/s13361-012-0379-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 02/29/2012] [Accepted: 03/16/2012] [Indexed: 05/31/2023]
Abstract
Tris(2,4,6-trimethoxyphenyl) phosphonium acetyl (TMPP-Ac) was previously introduced to improve the mass spectrometric sequence analysis of peptides by fixing a permanent charge at the N-termini. However, peptides containing arginine residues did not fragment efficiently after TMPP-Ac modification. In this work, we combine charge derivatization with photodissociation. The fragmentation of TMPP-derivatized peptides is greatly improved and a series of N-terminal fragments is generated with complete sequence information. Arginine has a special effect on the fragmentation of the TMPP tagged peptides when it is the N-terminal peptide residue. Theoretical and experimental results suggest that this is due to hydrogen transfer from the charged N-terminus to the hydrogen-deficient peptide sequence.
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Affiliation(s)
- Yi He
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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23
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Madsen JA, Cheng RR, Kaoud TS, Dalby KN, Makarov DE, Brodbelt JS. Charge-site-dependent dissociation of hydrogen-rich radical peptide cations upon vacuum UV photoexcitation. Chemistry 2012; 18:5374-83. [PMID: 22431222 DOI: 10.1002/chem.201103534] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Indexed: 11/06/2022]
Abstract
Here, 193 nm vacuum ultraviolet photodissociation (VUVPD) was used to investigate the fragmentation of hydrogen-rich radical peptide cations generated by electron transfer reactions. VUVPD offers new insight into the factors that drive radical- and photon-directed processes. The location of a basic Arg site influences photon-activated C(α)-C(O) bond cleavages of singly charged peptide radical cations, an outcome attributed to the initial conformation of the peptide as supported by molecular dynamics simulated annealing and the population of excited states upon UV excitation. This hybrid ETD/VUVPD method was employed to identify phosphorylation sites of the kinase domain of human TRPM7/ChaK1.
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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 78712, USA
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24
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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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25
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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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26
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Hao C, Le Blanc JCY, Verkerk UH, Siu KWM, Loboda AV. Ultraviolet photodissociation of protonated pharmaceuticals in a pressurized linear quadrupole ion trap. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:2262-2268. [PMID: 20623481 DOI: 10.1002/rcm.4633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Ultraviolet photodissociation (UVPD) was evaluated as a technique for generating ion fragmentation information that is alternative and/or complementary to the information obtained by collision-induced dissociation (CID). Ions trapped in a pressurized linear ion trap were dissociated using a 355 nm or a 266 nm pulsed laser. Comparisons of UVPD and CID spectra using a set of aromatic chromophore-containing compounds (desmethyl bosentan, haloperidol, nelfinavir) demonstrated distinct characteristic fragmentation patterns resulting from photodissociation. The wavelength of light and the pressure of the buffer gas in the UVPD cell are important parameters that control fragmentation pathways. The wavelength effect is related to the absorption cross section, location of the chromophore and the energy carried by one photon. Thus, UV irradiation wavelength affects fragmentation pathways as well as the fragmentation rate. The pressure effect can be explained by collisional quenching of 'slow' fragmentation pathways. We observed that higher pressure of the buffer gas during UVPD experiments highlights unique fragment ions by suppressing slow fragmentation pathways responsible for CID-like fragmentation patterns.
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Affiliation(s)
- Changtong Hao
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele St, Toronto, ON, Canada, M3J 1P3
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27
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Yoon SH, Moon JH, Kim MS. Dissociation mechanisms and implication for the presence of multiple conformations for peptide ions with arginine at the C-terminus: time-resolved photodissociation study. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:806-814. [PMID: 20564416 DOI: 10.1002/jms.1773] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Time-resolved photodissociation (PD) patterns of singly protonated peptides with arginine at the C-terminus (C-arg peptide ions) have been used to classify the dissociation channels into two categories, i.e. high-energy channels generating v, w and x and low-energy ones generating b, y and z. x + 1 formed by C(alpha)-CO cleavage seems to be the intermediate ion in high-energy channels just as a + 1 is for N-arg peptide ions. Difference in time-resolved pattern indicates that the two sets of channels, high- and low-energy ones, are not in direct competition. Noncompetitive dissociation is also indicated by the observation of anomalous effect of matrix used in matrix-assisted laser desorption ionization, a cooler matrix generating more high-energy product ions both in spontaneous dissociation and in PD. Results from detailed investigation suggest that the two sets of channels start from two (or more) different conformations.
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Affiliation(s)
- So Hee Yoon
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
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28
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Marchese R, Grandori R, Carloni P, Raugei S. On the zwitterionic nature of gas-phase peptides and protein ions. PLoS Comput Biol 2010; 6:e1000775. [PMID: 20463874 PMCID: PMC2865515 DOI: 10.1371/journal.pcbi.1000775] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 03/31/2010] [Indexed: 11/18/2022] Open
Abstract
Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation.
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Affiliation(s)
- Roberto Marchese
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
| | - Rita Grandori
- Department of Bioscience and Biotechnology, Milano-Bicocca, Milano, Italy
- * E-mail: (RG); (SR)
| | - Paolo Carloni
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
- Italian Institute of Technology (IIT), Trieste, Italy
- Computational Biophysics sector, German Research School for Simulation Science, FZ-Juelich and RWTH, Juelich, Germany
| | - Simone Raugei
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
- Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (RG); (SR)
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29
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Zhang L, Reilly JP. Peptide photodissociation with 157 nm light in a commercial tandem time-of-flight mass spectrometer. Anal Chem 2009; 81:7829-38. [PMID: 19702244 DOI: 10.1021/ac9012557] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photodissociation with 157 nm light was implemented in an ABI model 4700 matrix-assisted laser desorption ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer for peptide analysis. With a homemade computer program to control the light timing based on the m/z of each precursor ion, the photodissociation setup was seamlessly automated with the mass spectrometer. Peptide photodissociation in this apparatus yielded fragments similar to those observed in previous experiments with a home-built tandem-TOF mass spectrometer. Peptides having arginine at their C-termini yielded high-energy x-, v-, and w- type fragments, while peptides with N-terminal arginine produced many a- and d- type ions. Abundant immonium ions were also generated. High-quality photodissociation spectra were obtained with as little as 5 fmol of peptides. In the analysis of various tryptic peptides, photodissociation provided much more sequence information than the conventional TOF-TOF collision induced dissociation (CID). Because of the high fragmentation efficiency, sensitivity was not sacrificed to achieve this.
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Affiliation(s)
- Liangyi Zhang
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, USA
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30
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Yoon SH, Moon JH, Chung YJ, Kim MS. Influence of basic residues on dissociation kinetics and dynamics of singly protonated peptides: time-resolved photodissociation study. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:1532-1537. [PMID: 19753580 DOI: 10.1002/jms.1670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Product ion yields in postsource decay and time-resolved photodissociation at 193 and 266 nm were measured for some peptide ions with lysine ([KF6 + H]+, [F6K + H]+, and [F3KF3 + H]+) formed by matrix-assisted laser desorption ionization. The critical energy (E0) and entropy (DeltaS(double dagger)) were determined by RRKM fitting of the data. The results were similar to those found previously for peptide ions with histidine. To summarize, the presence of a basic residue, histidine or lysine, inside a peptide ion retarded its dissociation by lowering DeltaS(double dagger). On the basis of highly negative DeltaS(double dagger), presence of intramolecular interaction involving a basic group in the transition structure was proposed.
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Affiliation(s)
- So Hee Yoon
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
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31
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Brodbelt JS, Wilson JJ. Infrared multiphoton dissociation in quadrupole ion traps. MASS SPECTROMETRY REVIEWS 2009; 28:390-424. [PMID: 19294735 DOI: 10.1002/mas.20216] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The development of new ion activation techniques continues to be a dynamic area of scientific discovery, in part to complement the tremendous innovations in ionization methods that have allowed the mass spectrometric analysis of an enormous array of molecules. Ion activation/dissociation provides key information about ion structures, binding energies, and differentiation of isomers, as well as affording a primary means of identifying compounds in mixtures. Numerous new activation methods have emerged over the past two decades in an effort to develop alternatives to collisional activated dissociation, the gold standard for providing structurally diagnostic fragmentation patterns. Collisional activated dissociation does not always offer sufficiently high or controllable energy deposition, thus rendering it less useful for certain classes of molecules, such as large proteins or macromolecular complexes. Photodissociation is one of the most promising alternatives and is readily implemented in ion trapping and time-of-flight mass spectrometers. Photodissociation generally entails using a laser to irradiate ions with UV, visible, or IR photons, thus resulting in internal energy deposition based on the number and wavelengths of the photons. The activation process can be extremely rapid and efficient, as well as having the potential for high total energy deposition. This review describes infrared multiphoton dissociation in quadrupole ion trap mass spectrometry. A comparison of photodissociation and collisional activated dissociation is covered, in addition to some of the methods to increase photodissociation efficiency. Numerous applications of IRMPD are discussed as well, including ones related to the analysis of drugs, peptides, nucleic acids, and oligosaccharides.
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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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32
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Abstract
Mass spectrometric identification of all types of molecules relies on the observation and interpretation of ion fragmentation patterns. Peptides, proteins, carbohydrates, and nucleic acids that are often found as components of complex biological samples represent particularly important challenges. The most common strategies for fragmenting biomolecular ions include low- and high-energy collisional activation, post-source decay, and electron capture or transfer dissociation. Each of these methods has its own idiosyncrasies and advantages but encounters problems with some types of samples. Novel fragmentation methods that can offer improvements are always desirable. One approach that has been under study for years but is not yet incorporated into a commercial instrument is ultraviolet photofragmentation. This review discusses experimental results on various biological molecules that have been generated by several research groups using different light wavelengths and mass analyzers. Work involving short-wavelength vacuum ultraviolet light is particularly emphasized. The characteristics of photofragmentation are examined and its advantages summarized.
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Affiliation(s)
- James P Reilly
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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Yoon SH, Chung YJ, Kim MS. Time-resolved photodissociation of singly protonated peptides with an arginine at the N-terminus: a statistical interpretation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:645-655. [PMID: 18356076 DOI: 10.1016/j.jasms.2008.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 02/14/2008] [Accepted: 02/16/2008] [Indexed: 05/26/2023]
Abstract
Time-evolution of product ion signals in ultraviolet photodissociation (UV-PD) of singly protonated peptides with an arginine at the N-terminus was investigated by using a tandem time-of-flight mass spectrometer equipped with a cell floated at high voltage. Observation of different time-evolution patterns for different product ion types--an apparently nonstatistical behavior--could be explained within the statistical framework by invoking consecutive formation of some product ions and broad internal energy distributions for precursor ions. a(n) + 1 and b(n) ions were taken as the primary product ions from this type of peptide ions. Spectral characteristics in post-source decay, UV-PD, and collisionally activated dissociation at low and high kinetic energies could be explained via rough statistical calculation of rate constants. Specifically, the striking characteristics in high-energy CAD and UV-PD--dominance of a(n) and d(n) formed via a(n) + 1--were not due to the peculiarity of the excitation processes themselves, but due to quenching of the b(n) channels caused by the presence of arginine.
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Affiliation(s)
- So Hee Yoon
- Department of Chemistry, Seoul National University, Seoul, Korea
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Wilson JJ, Kirkovits GJ, Sessler JL, Brodbelt JS. Photodissociation of non-covalent peptide-crown ether complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:257-60. [PMID: 18077179 PMCID: PMC2288744 DOI: 10.1016/j.jasms.2007.10.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 10/29/2007] [Accepted: 10/29/2007] [Indexed: 05/25/2023]
Abstract
Highly chromogenic 18-crown-6-dipyrrolylquinoxaline coordinates primary amines of peptides, forming non-covalent complexes that can be transferred to the gas-phase by electrospray ionization. The appended chromogenic crown ether facilitates efficient energy transfer to the peptide upon ultraviolet irradiation in the gas phase, resulting in diagnostic peptide fragmentation. Collisional-activated dissociation and infrared multiphoton dissociation of these non-covalent complexes result only in their disassembly with the charge retained on either the peptide or crown ether, yielding no sequence ions. Upon UV photon absorption the intermolecular energy transfer is facilitated by the fast activation timescale of ultraviolet photodissociation (<10 ns) and by the collectively strong hydrogen bonding between the crown ether and peptide, thus allowing effective transfer of energy to the peptide moiety before disruption of the intermolecular hydrogen bonds.
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Affiliation(s)
- Jeffrey J Wilson
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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Yoon SH, Kim MS. Development of a time-resolved method for photodissociation mechanistic study of protonated peptides: use of a voltage-floated cell in a tandem time-of-flight mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1729-39. [PMID: 17702598 DOI: 10.1016/j.jasms.2007.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 06/26/2007] [Accepted: 07/03/2007] [Indexed: 05/16/2023]
Abstract
Photodissociation at 266 nm of some protonated peptides was investigated using a tandem-TOF spectrometer equipped with a cell near its first time focal point where the laser was irradiated. When a high voltage was applied to the cell, each product ion peak split into several components with different flight times. One of these was due to in-cell direct formation of the product ion and another due to post-cell formation. Those in between were due to consecutive dissociations, the first steps of which occurred inside the cell and the second steps outside the cell. A method based on flight time calculation was developed to analyze these components and to identify the intermediate ion for each consecutive component. The technique allows time-resolved photodissociation mechanistic studies on a 100-ns timescale.
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Affiliation(s)
- So Hee Yoon
- Department of Chemistry, Seoul National University, Seoul, Korea
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Wilson JJ, Brodbelt JS. MS/MS simplification by 355 nm ultraviolet photodissociation of chromophore-derivatized peptides in a quadrupole ion trap. Anal Chem 2007; 79:7883-92. [PMID: 17845006 DOI: 10.1021/ac071241t] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet photodissociation (UVPD) of chromophore-modified peptides enhances the capabilities for de novo sequencing in a quadrupole ion trap mass spectrometer. Attachment of UV chromophores allows efficient photoactivation of not only the precursor ions but also any fragments that retain the chromophore functionality. For doubly protonated peptides, UVPD leads to a vast reduction in MS/MS complexity. The array of b and y ions typically seen upon collisionally activated dissociation is reduced to a single series of either y or b ions by UVPD depending on the location of the chromophore (i.e., N- or C-terminus). The sulfonation reagent Alexa Fluor 350 (AF350) provided the best overall results for the singly and doubly charged peptides by UVPD. The nonsulfonated analogue of AF350, 7-amino-4-methylcoumarin-3-acetic acid, also led to simplified spectra for doubly charged, but not singly charged, peptides by UVPD. Dinitrophenyl-peptides also yielded simplified spectra by UVPD albeit with a small amount of internal fragments accompanying the series of diagnostic y ions. The success of this MS/MS simplification process stems from extensive secondary fragmentation of any chromophore-containing fragments upon exposure to subsequent laser pulses. Energy-variable UVPD reveals that the abundances of non-chromophore-containing y fragment ions increase linearly with laser pulse energy, suggesting secondary dissociation of these species is insignificant. The abundances of chromophore-containing a/b fragment ions follow a quadratic trend due to the extensive secondary fragmentation at higher laser energies or multiple pulses.
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Affiliation(s)
- Jeffrey J Wilson
- Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
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Thompson MS, Cui W, Reilly JP. Factors that impact the vacuum ultraviolet photofragmentation of peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1439-52. [PMID: 17543535 DOI: 10.1016/j.jasms.2007.04.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Revised: 04/20/2007] [Accepted: 04/24/2007] [Indexed: 05/15/2023]
Abstract
Several groups have investigated the photodissociation of peptide ions with ultraviolet light. Significant differences have been reported with 157 and 193 nm excitation. Recent studies have shown that the mass analyzer can also influence the observed photofragment distribution. Comparison of experiments using different peptides, wavelengths, and mass analyzers is undesirably complicated. In the present work, several peptides are analyzed with both 157 and 193 nm photodissociation in tandem-TOF and linear ion trap mass spectrometers. The results indicate that the fragment ion distribution can be influenced by both the photodissociation wavelength and the mass analyzer. The two wavelengths generate similar spectra in an ion trap but quite different results in a tandem-TOF instrument.
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Affiliation(s)
- Matthew S Thompson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001, USA
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:266-277. [PMID: 17262881 DOI: 10.1002/jms.1071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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Moon JH, Shin YS, Cha HJ, Kim MS. Photodissociation at 193 nm of some singly protonated peptides and proteins with m/z 2000-9000 using a tandem time-of-flight mass spectrometer equipped with a second source for delayed extraction/post-acceleration of product ions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:359-68. [PMID: 17206742 DOI: 10.1002/rcm.2855] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A tandem time-of-flight mass spectrometer was built for photodissociation (PD) of singly protonated peptides and small proteins generated by matrix-assisted laser desorption/ionization. PD was performed in a second source after deceleration of precursor ions. The delayed extraction/post-acceleration scheme was used for the product ions. For the PD at 193 nm of small singly protonated peptides, the present instrument showed much better sensitivity and resolution for product ions than the previous one (Moon JH, Yoon SH, Kim MS, Bull. Korean Chem. Soc. 2005; 26: 763) even though the overall spectral patterns obtained with the two instruments were similar. The present instrument was inferior in precursor ion selection and background noise level. PD was achieved for precursor ions as large as the singly protonated ubiquitin (m/z 8560.63), indicating that the photoexcitation is capable of supplying a sufficient amount of internal energy to dissociate large singly protonated proteins. As the precursor ion m/z increased, however, product ion signals deteriorated rather rapidly. As in the PD of small peptide ions with m/z around 1000, the types of the product ions generated from singly protonated peptides with m/z in the range 2000-4000 were mostly determined by the positions of arginine residues. Namely, a(n) and d(n) ions dominated when an arginine residue(s) was near the N-terminus while v(n), w(n), x(n) and y(n) dominated when the same residue(s) was near the C-terminus. In addition, d(n), v(n) and w(n) ions were generated according to the correlation rules previously observed in the collisionally activated dissociation. Isoleucine and leucine isomers could be easily distinguished based on the w(n) and d(n) ions.
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Affiliation(s)
- Jeong Hee Moon
- School of Chemistry, Seoul National University, Seoul 151-742, Korea
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Choi KM, Yoon SH, Sun M, Oh JY, Moon JH, Kim MS. Characteristics of photodissociation at 193 nm of singly protonated peptides generated by matrix-assisted laser desorption ionization (MALDI). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1643-53. [PMID: 16934996 DOI: 10.1016/j.jasms.2006.07.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Revised: 07/15/2006] [Accepted: 07/19/2006] [Indexed: 05/11/2023]
Abstract
Photodissociation (PD) at 193 nm of various singly protonated peptides was investigated. These include peptides with an arginine residue at the C-terminus, N-terminus, at both termini, inside the chain, and those without an arginine residue. Monoisotopomeric selection was made for the precursor ions. Interference from the post-source decay (PSD) product signals was reduced as much as possible by using the deflection system (reported previously) and subtracting the remaining signals from the laser-on signals. The presence of an arginine residue and its position inside the peptide were found to significantly affect the PD spectra, as reported previously. Presence of a proline, aspartic acid, or glutamic acid residue hardly affected the PD spectral patterns. By comparing the PD spectra obtained at a few different wavelengths, it is concluded that the dissociation of the photoexcited ions occurs in their ground electronic states. Tentative explanations for the observed spectral correlations based on the statistical picture for the reactions are also presented.
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Affiliation(s)
- Kyung Mi Choi
- National Creative Research Initiative Center for Control of Reaction Dynamics and School of Chemistry, Seoul National University, Seoul, Korea
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