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Li HF, Zhao J, Cao W, Zhang W, Xia Y, Ouyang Z. Site-Specific Photochemical Reaction for Improved C=C Location Analysis of Unsaturated Lipids by Ultraviolet Photodissociation. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9783602. [PMID: 35252873 PMCID: PMC8859641 DOI: 10.34133/2022/9783602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/16/2022] [Indexed: 11/16/2022]
Abstract
Unraveling the complexity of the lipidome requires the development of novel approaches to facilitate structural identification and characterization of lipid species with isomer-level discrimination. Ultraviolet photodissociation tandem mass spectrometry (UVPD MS/MS) is a promising tool for structure determination of lipids. The sensitivity of UVPD for lipid analysis however is limited mainly due to weak absorption of UV photons by a C=C. Herein, a C=C site-specific derivatization, the Paternò-Büchi (PB) reaction, was used to incorporate a chromophore to the C=C moiety in fatty acyls, leading to significantly improved UVPD efficiency and sensitivity for pinpointing C=C locations. The wavelength-dependent photodissociation of the PB products demonstrated 4-CF3-benzophenone as the best reagent for UVPD in terms of the efficiency of generating C=C diagnostic fragments and simplicity for C=C location assignments. We demonstrated the effectiveness of this approach for the shotgun profiling of C=C location isomers in different lipid classes from complex lipid extracts, highlighting its potential to advancing the identification of the C=C bond locations in unsaturated lipids.
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Affiliation(s)
- Hai-Fang Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Jing Zhao
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Wenbo Cao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
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2
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Narreddula VR, McKinnon BI, Marlton SJP, Marshall DL, Boase NRB, Poad BLJ, Trevitt AJ, Mitchell TW, Blanksby SJ. Next-generation derivatization reagents optimized for enhanced product ion formation in photodissociation-mass spectrometry of fatty acids. Analyst 2021; 146:156-169. [DOI: 10.1039/d0an01840f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Next-generation derivatives for photodissociation-mass spectrometry for fatty acids generating photoproduct yields of up to 97% at 266 nm.
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Affiliation(s)
- Venkateswara R. Narreddula
- School of Chemistry and Physics
- Science and Engineering Faculty
- Queensland University of Technology
- Brisbane
- Australia
| | - Benjamin I. McKinnon
- Molecular Horizons and School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - Samuel J. P. Marlton
- Molecular Horizons and School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - David L. Marshall
- Central Analytical Research Facility
- Institute for Future Environments
- Queensland University of Technology
- Brisbane
- Australia
| | - Nathan R. B. Boase
- School of Chemistry and Physics
- Science and Engineering Faculty
- Queensland University of Technology
- Brisbane
- Australia
| | - Berwyck L. J. Poad
- Central Analytical Research Facility
- Institute for Future Environments
- Queensland University of Technology
- Brisbane
- Australia
| | - Adam J. Trevitt
- Molecular Horizons and School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - Todd W. Mitchell
- School of Medicine
- University of Wollongong
- Wollongong
- Australia
- Illawarra Health and Medical Research Institute
| | - Stephen J. Blanksby
- School of Chemistry and Physics
- Science and Engineering Faculty
- Queensland University of Technology
- Brisbane
- Australia
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3
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Narreddula VR, Sadowski P, Boase NRB, Marshall DL, Poad BLJ, Trevitt AJ, Mitchell TW, Blanksby SJ. Structural elucidation of hydroxy fatty acids by photodissociation mass spectrometry with photolabile derivatives. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8741. [PMID: 32012356 DOI: 10.1002/rcm.8741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Eicosanoids are short-lived bio-responsive lipids produced locally from oxidation of polyunsaturated fatty acids (FAs) via a cascade of enzymatic or free radical reactions. Alterations in the composition and concentration of eicosanoids are indicative of inflammation responses and there is strong interest in developing analytical methods for the sensitive and selective detection of these lipids in biological mixtures. Most eicosanoids are hydroxy FAs (HFAs), which present a particular analytical challenge due to the presence of regioisomers arising from differing locations of hydroxylation and unsaturation within their structures. METHODS In this study, the recently developed derivatization reagent 1-(3-(aminomethyl)-4-iodophenyl)pyridin-1-ium (4-I-AMPP+ ) was applied to a representative set of HFAs including bioactive eicosanoids. Photodissociation (PD) mass spectra obtained at 266 nm of 4-I-AMPP+ -modified HFAs exhibit abundant product ions arising from photolysis of the aryl-iodide bond within the derivative with subsequent migration of the radical to the hydroxyl group promoting fragmentation of the FA chain and facilitating structural assignment. RESULTS Representative polyunsaturated HFAs (from the hydroxyeicosatetraenoic acid and hydroxyeicosapentaenoic acid families) were derivatized with 4-I-AMPP+ and subjected to a reversed-phase liquid chromatography workflow that afforded chromatographic resolution of isomers in conjunction with structurally diagnostic PD mass spectra. CONCLUSIONS PD of these complex HFAs was found to be sensitive to the locations of hydroxyl groups and carbon-carbon double bonds, which are structural properties strongly associated with the biosynthetic origins of these lipid mediators.
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Affiliation(s)
- Venkateswara R Narreddula
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Nathan R B Boase
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - David L Marshall
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Berwyck L J Poad
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Adam J Trevitt
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Todd W Mitchell
- School of Medicine, University of Wollongong, Wollongong, NSW, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Stephen J Blanksby
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
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4
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Wäldchen F, Becher S, Esch P, Kompauer M, Heiles S. Selective phosphatidylcholine double bond fragmentation and localisation using Paternò-Büchi reactions and ultraviolet photodissociation. Analyst 2018; 142:4744-4755. [PMID: 29142996 DOI: 10.1039/c7an01158j] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effect of double bond functionalisation for selective double bond localisation by ultraviolet photodissociation of phosphatidylcholines is investigated. Paternò-Büchi reactions in nanoESI emitter tips enable attachment of acetophenone to double bonds of unsaturated phosphatidylcholines after 100 s of 254 nm light irradiation with about 50-80% reaction yield. Functionalized phosphatidylcholines dissociate upon 266 nm irradiation yielding double bond selective fragment ions in contrast to results for ultraviolet photodissociation of unmodified lipids. Ultraviolet photodissociation of Paternò-Büchi modified lipids results in a selectivity increase of up to 2.2 towards double bond localisation compared collision-induced dissociation experiments. Double bond localisation is also possible with ultraviolet photodissociation when alkali metal ion attachment to Paternò-Büchi modified phosphatidylcholines occurs in contrast to classic collision-induced dissociation experiments. The developed methodology is used to differentiate lipid double bond isomers and applied to phosphatidylcholines from egg yolk to identify 15 phosphatidylcholines. Results from this study demonstrate that locally depositing energy in close vicinity to cleavable bonds via ultraviolet photodissociation can result in increased dissociation selectivity. This method can help to disentangle contributions from different structural elements in complex tandem mass spectra of lipids and aid to the structural characterization of phospholipids in a "top-down" approach.
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Affiliation(s)
- Fabian Wäldchen
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
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5
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Giuliani A, Williams JP, Green MR. Extreme Ultraviolet Radiation: A Means of Ion Activation for Tandem Mass Spectrometry. Anal Chem 2018; 90:7176-7180. [DOI: 10.1021/acs.analchem.8b01789] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandre Giuliani
- Synchrotron SOLEIL, L’Orme des Merisiers, Gif-sur-Yvette F-91190, France
- UAR 1008 CEPIA, INRA, Nantes F-44316, France
| | | | - Martin R. Green
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, U.K
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6
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Ryan E, Nguyen CQN, Shiea C, Reid GE. Detailed Structural Characterization of Sphingolipids via 193 nm Ultraviolet Photodissociation and Ultra High Resolution Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1406-1419. [PMID: 28455688 DOI: 10.1007/s13361-017-1668-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 05/29/2023]
Abstract
Sphingolipids serve not only as components of cellular membranes but also as bioactive mediators of numerous cellular functions. As the biological activities of these lipids are dependent on their structures, and due to the limitations of conventional ion activation methods employed during tandem mass spectrometry (MS/MS), there is a recognized need for the development of improved structure-specific methods for their comprehensive identification and characterization. Here, positive-ionization mode 193 nm ultraviolet photodissociation (UVPD)-MS/MS has been implemented for the detailed structural characterization of lipid species from a range of sphingolipid classes introduced to the mass spectrometer via electrospray ionization as their lithiated or protonated adducts. These include sphingosine d18:1(4E), dihydrosphingosine (sphinganine) d18:0, sphingadiene d18:2(4E,11Z), the isomeric sphingolipids ceramide d18:1(4E)/18:0 and dihydroceramide d18:0/18:1(9Z), ceramide-1-phosphate d18:1(4Z)/16:0, sphingomyelin d18:1(4E)/18:1(9Z) the glycosphingolipids galactosyl ceramide d18:1(4E)/24:1(15Z) and lactosyl ceramide d18:1(4E)/24:0, and several endogenous lipids present within a porcine brain total lipid extract. In addition to the product ions formed by higher energy collision dissociation (HCD), UVPD is shown to yield a series of novel structurally diagnostic product ions resulting from cleavage of both sphingosine carbon-carbon and acyl chain carbon-carbon double bonds for direct localization of site(s) of unsaturation, as well as via diagnostic cleavages of the sphingosine backbone and N-C amide bond linkages. With activation timescales and dissociation efficiencies similar to those found in conventional MS/MS strategies, this approach is therefore a promising new tool in the arsenal of ion activation techniques toward providing complete structural elucidation in automated, high-throughput lipid analysis workflows. Graphical Abstract ᅟ.
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Affiliation(s)
- Eileen Ryan
- School of Chemistry, University of Melbourne, Parkville, Victoria, 3010, Australia
| | | | - Christopher Shiea
- School of Chemistry, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gavin E Reid
- School of Chemistry, University of Melbourne, Parkville, Victoria, 3010, Australia.
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
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7
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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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8
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O'Brien JP, Li W, Zhang Y, Brodbelt JS. Characterization of native protein complexes using ultraviolet photodissociation mass spectrometry. J Am Chem Soc 2014; 136:12920-8. [PMID: 25148649 DOI: 10.1021/ja505217w] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry (MS) was used to characterize the sequences of proteins in native protein-ligand and protein-protein complexes and to provide auxiliary information about the binding sites of the ligands and protein-protein interfaces. UVPD outperformed collisional induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron transfer dissociation (ETD) in terms of yielding the most comprehensive diagnostic primary sequence information about the proteins in the complexes. UVPD also generated noncovalent fragment ions containing a portion of the protein still bound to the ligand which revealed some insight into the nature of the binding sites of myoglobin/heme, eIF4E/m(7)GTP, and human peptidyl-prolyl cis-trans isomerase 1 (Pin1) in complex with the peptide derived from the C-terminal domain of RNA polymerase II (CTD). Noncovalently bound protein-protein fragment ions from oligomeric β-lactoglobulin dimers and hexameric insulin complexes were also produced upon UVPD, providing some illumination of tertiary and quaternary protein structural features.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, ‡Department of Molecular Biosciences, and §Institute for Cellular and Molecular Biology, The University of Texas at Austin , 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
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9
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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
![]()
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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10
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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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11
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Liu X, Li YF, Bohrer BC, Arnold RJ, Radivojac P, Tang H, Reilly JP. Investigation of VUV Photodissociation Propensities Using Peptide Libraries. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 308:142-154. [PMID: 22125417 PMCID: PMC3224043 DOI: 10.1016/j.ijms.2011.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PSD does not usually generate a complete series of y-type ions, particularly at high mass, and this is a limitation for de novo sequencing algorithms. It is demonstrated that b(2) and b(3) ions can be used to help assign high mass x(N-2) and x(N-3) fragments that are found in vacuum ultraviolet (VUV) photofragmentation experiments. In addition, v(N)-type ion fragments with side chain loss from the N-terminal residue often enable confirmation of N-terminal amino acids. Libraries containing several thousand peptides were examined using photodissociation in a MALDI-TOF/TOF instrument. 1345 photodissociation spectra with a high S/N ratio were interpreted.
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12
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Ko BJ, Brodbelt JS. 193 nm Ultraviolet Photodissociation of Deprotonated Sialylated Oligosaccharides. Anal Chem 2011; 83:8192-200. [DOI: 10.1021/ac201751u] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Byoung Joon Ko
- Departments of †Chemical Engineering, and ‡Chemistry and Biochemistry, 1 University Station A5300, University of Texas at Austin, Austin, Texas, United States
| | - Jennifer S. Brodbelt
- Departments of †Chemical Engineering, and ‡Chemistry and Biochemistry, 1 University Station A5300, University of Texas at Austin, Austin, Texas, United States
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13
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Zhang L, Reilly JP. De novo sequencing of tryptic peptides derived from Deinococcus radiodurans ribosomal proteins using 157 nm photodissociation MALDI TOF/TOF mass spectrometry. J Proteome Res 2010; 9:3025-34. [PMID: 20377247 DOI: 10.1021/pr901206j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vacuum ultraviolet photodissociation of peptide ions in a matrix assisted laser desorption ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer is used to characterize peptide mixtures derived from Deinococcus radiodurans ribosomal proteins. Tryptic peptides from 52 proteins were separated by reverse-phase liquid chromatography and spotted onto a MALDI plate. From 192 sample spots, 492 peptide ions were isolated, fragmented by both photodissociation and postsource decay (PSD), and then de novo sequenced. Three-hundred seventy-two peptides yielded sequences with 5 or more amino acids. Homology searches of these sequences against the whole bacterial proteome identified 49 ribosomal proteins, 45 of which matched with two or more peptides. Peptide de novo sequencing identified slightly more proteins than conventional database searches using Mascot and was particularly advantageous in identifying unexpected peptide modifications. In the present analysis, 52 peptide modifications were identified by de novo sequencing, most of which were not recognized by database searches.
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Affiliation(s)
- Liangyi Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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14
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Blanksby SJ, Mitchell TW. Advances in mass spectrometry for lipidomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2010; 3:433-65. [PMID: 20636050 DOI: 10.1146/annurev.anchem.111808.073705] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Recent expansion in research in the field of lipidomics has been driven by the development of new mass spectrometric tools and protocols for the identification and quantification of molecular lipids in complex matrices. Although there are similarities between the field of lipidomics and the allied field of mass spectrometry (e.g., proteomics), lipids present some unique advantages and challenges for mass spectrometric analysis. The application of electrospray ionization to crude lipid extracts without prior fractionation-the so-called shotgun approach-is one such example, as it has perhaps been more successfully applied in lipidomics than in any other discipline. Conversely, the diverse molecular structure of lipids means that collision-induced dissociation alone may be limited in providing unique descriptions of complex lipid structures, and the development of additional, complementary tools for ion activation and analysis is required to overcome these challenges. In this article, we discuss the state of the art in lipid mass spectrometry and highlight several areas in which current approaches are deficient and further innovation is required.
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15
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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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16
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Kim TY, Schwartz JC, Reilly JP. Development of a Linear Ion Trap/Orthogonal-Time-of-Flight Mass Spectrometer for Time-Dependent Observation of Product Ions by Ultraviolet Photodissociation of Peptide Ions. Anal Chem 2009; 81:8809-17. [DOI: 10.1021/ac9013258] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tae-Young Kim
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, and Thermo Electron, 355 River Oaks Parkway, San Jose, California 95134
| | - Jae C. Schwartz
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, and Thermo Electron, 355 River Oaks Parkway, San Jose, California 95134
| | - James P. Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, and Thermo Electron, 355 River Oaks Parkway, San Jose, California 95134
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17
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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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Zhang L, Reilly JP. Extracting both peptide sequence and glycan structural information by 157 nm photodissociation of N-linked glycopeptides. J Proteome Res 2009; 8:734-42. [PMID: 19113943 DOI: 10.1021/pr800766f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-of-flight (TOF) and linear ion trap mass spectrometers. Singly charged glycopeptides yielded abundant peptide and glycan fragments. The peptide fragments included a series of x-, y-, v-, and w- ions with the glycan remaining intact. These provide information about the peptide sequence and the glycosylation site. In addition to glycosidic fragments, abundant cross-ring glycan fragments that are not observed in low-energy CID were detected. These fragments provide insight into the glycan sequence and linkages. Doubly charged glycopeptides generated by nanospray in the linear ion trap mass spectrometer also yielded peptide and glycan fragments. However, the former were dominated by low-energy fragments such as b- and y- type ions while glycan was primarily cleaved at glycosidic bonds.
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Affiliation(s)
- Liangyi Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Devakumar A, Mechref Y, Kang P, Novotny MV, Reilly JP. Identification of isomeric N-glycan structures by mass spectrometry with 157 nm laser-induced photofragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1027-40. [PMID: 18487060 PMCID: PMC2523269 DOI: 10.1016/j.jasms.2008.03.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 03/07/2008] [Accepted: 03/07/2008] [Indexed: 05/03/2023]
Abstract
Characterization of structural isomers has become increasingly important and extremely challenging in glycobiology. This communication demonstrates the capability of ion-trap mass spectrometry in conjunction with 157 nm photofragmentation to identify different structural isomers of permethylated N-glycans derived from ovalbumin without chromatographic separation. The results are compared with collision-induced dissociation (CID) experiments. Photodissociation generates extensive cross-ring fragment ions as well as diagnostic glycosidic product ions that are not usually observed in CID MS/MS experiments. The detection of these product ions aids in characterizing indigenous glycan isomers. The ion trap facilitates MS(n) experiments on the diagnostic glycosidic fragments and cross-ring product ions generated through photofragmentation, thus allowing unambiguous assignment of all of the isomeric structures associated with the model glycoprotein used in this study. Photofragmentation is demonstrated to be a powerful technique for the structural characterization of glycans.
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Affiliation(s)
| | | | | | | | - James P. Reilly
- * Corresponding Author: James P. Reilly, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA, E-mail:
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