1
|
Lembo A, Molinaro A, De Castro C, Berti F, Biagini M. Impact of glycosylation on viral vaccines. Carbohydr Polym 2024; 342:122402. [PMID: 39048237 DOI: 10.1016/j.carbpol.2024.122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
Glycosylation is the most prominent modification important for vaccines and its specific pattern depends on several factors that need to be considered when developing a new biopharmaceutical. Tailor-made glycosylation can be exploited to develop more effective and safer vaccines; for this reason, a deep understanding of both glycoengineering strategies and glycans structures and functions is required. In this review we discuss the recent advances concerning glycoprotein expression systems and the explanation of glycans immunomodulation mechanisms. Furthermore, we highlight how glycans tune the immunological properties among different vaccines platforms (whole virus, recombinant protein, nucleic acid), also comparing commercially available formulations and describing the state-of-the-art analytical technologies for glycosylation analysis. The whole review stresses the aspect of glycoprotein glycans as a potential tool to overcome nowadays medical needs in vaccine field.
Collapse
Affiliation(s)
- Antonio Lembo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy; GSK, Siena, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
| | | | | |
Collapse
|
2
|
Butalewicz JP, Escobar EE, Wootton CA, Theisen A, Park MA, Seeley EH, Brodbelt JS. Conformational Characterization of Peptides and Proteins by 193 nm Ultraviolet Photodissociation in the Collision Cell of a Trapped Ion Mobility Spectrometry-Time-of-Flight Mass Spectrometer. Anal Chem 2024. [PMID: 39365147 DOI: 10.1021/acs.analchem.4c02686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Ultraviolet photodissociation (UVPD) has been shown to be a versatile ion activation strategy for the characterization of peptides and intact proteins among other classes of biological molecules. Combining the high-performance mass spectrometry (MS/MS) capabilities of UVPD with the high-resolution separation of trapped ion mobility spectrometry (TIMS) presents an opportunity for enhanced structural elucidation of biological molecules. In the present work, we integrate a 193 nm excimer laser in a TIMS-time-of-flight (TIMS-TOF) mass spectrometer for UVPD in the collision cell and use it for the analysis of several mass-mobility-selected species of ubiquitin and myoglobin. The resultant data displayed differences in fragmentation that could be correlated with changes in protein conformation. Additionally, this mobility-resolved UVPD strategy was applied to collision-induced unfolded ions of ubiquitin to follow changes in fragmentation patterns relating to the extent of protein unfolding. This platform and methodology offer new opportunities for exploring how conformational variations are manifested in the fragmentation patterns of gas-phase ions.
Collapse
Affiliation(s)
- Jamie P Butalewicz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Edwin E Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Alina Theisen
- Bruker Daltonics GmbH & Co. KG, Bremen 28359, Germany
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Erin H Seeley
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
3
|
Gutiérrez-Quintanilla A, Moge B, Compagnon I, Noble JA. Vibrational and electronic spectra of protonated vanillin: exploring protonation sites and isomerisation. Phys Chem Chem Phys 2024; 26:15358-15368. [PMID: 38767194 DOI: 10.1039/d3cp05573f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Photofragmentation spectra of protonated vanillin produced under electrospray ionisation (ESI) conditions have been recorded in the 3000-3700 cm-1 (vibrational) and 225-460 nm (electronic) ranges, using room temperature IRMPD (infrared multiphoton dissociation) and cryogenic UVPD (ultraviolet photodissociation) spectroscopies, respectively. The cold (∼50 K) electronic UVPD spectrum exhibits very well resolved vibrational structure for the S1 ← S0 and S3 ← S0 transitions, suggesting long excited state dynamics, similar to its simplest analogue, protonated benzaldehyde. The experimental data were combined with theoretical calculations to determine the protonation site and configurational isomer observed in the experiments.
Collapse
Affiliation(s)
- Alejandro Gutiérrez-Quintanilla
- CNRS, Aix Marseille Univ., PIIM, Physique des Interactions Ioniques et Moléculaires, UMR 7345, 13397 Marseille, France.
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Baptiste Moge
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Isabelle Compagnon
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Jennifer A Noble
- CNRS, Aix Marseille Univ., PIIM, Physique des Interactions Ioniques et Moléculaires, UMR 7345, 13397 Marseille, France.
| |
Collapse
|
4
|
Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
5
|
Smyrnakis A, Levin N, Kosmopoulou M, Jha A, Fort K, Makarov A, Papanastasiou D, Mohammed S. Characterization of an Omnitrap-Orbitrap Platform Equipped with Infrared Multiphoton Dissociation, Ultraviolet Photodissociation, and Electron Capture Dissociation for the Analysis of Peptides and Proteins. Anal Chem 2023; 95:12039-12046. [PMID: 37534599 PMCID: PMC10433246 DOI: 10.1021/acs.analchem.3c01899] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
We describe an instrument configuration based on the Orbitrap Exploris 480 mass spectrometer that has been coupled to an Omnitrap platform. The Omnitrap possesses three distinct ion-activation regions that can be used to perform resonant-based collision-induced dissociation, several forms of electron-associated fragmentation, and ultraviolet photodissociation. Each section can also be combined with infrared multiphoton dissociation. In this work, we demonstrate all these modes of operation in a range of peptides and proteins. The results show that this instrument configuration produces similar data to previous implementations of each activation technique and at similar efficiency levels. We demonstrate that this unique instrument configuration is extremely versatile for the investigation of polypeptides.
Collapse
Affiliation(s)
- Athanasios Smyrnakis
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Nikita Levin
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Pharmacology, University of Oxford, OX1 3QT Oxford, U.K.
| | - Mariangela Kosmopoulou
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Ajay Jha
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Pharmacology, University of Oxford, OX1 3QT Oxford, U.K.
| | - Kyle Fort
- Thermo
Fisher Scientific, 28199 Bremen, Germany
| | | | - Dimitris Papanastasiou
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Shabaz Mohammed
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Biochemistry, University of Oxford, OX1 3QU Oxford, U.K.
- Department
of Chemistry, University of Oxford, OX1 3TA Oxford, U.K.
| |
Collapse
|
6
|
Theisen A, Wootton CA, Haris A, Morgan TE, Lam YPY, Barrow MP, O’Connor PB. Enhancing Biomolecule Analysis and 2DMS Experiments by Implementation of (Activated Ion) 193 nm UVPD on a FT-ICR Mass Spectrometer. Anal Chem 2022; 94:15631-15638. [DOI: 10.1021/acs.analchem.2c02354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Anisha Haris
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Tomos E. Morgan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Yuko P. Y. Lam
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Mark P. Barrow
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Peter B. O’Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| |
Collapse
|
7
|
Papanastasiou D, Kounadis D, Lekkas A, Orfanopoulos I, Mpozatzidis A, Smyrnakis A, Panagiotopoulos E, Kosmopoulou M, Reinhardt-Szyba M, Fort K, Makarov A, Zubarev RA. The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1990-2007. [PMID: 36113052 PMCID: PMC9850925 DOI: 10.1021/jasms.2c00214] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Multidimensional multiple-stage tandem processing of ions is demonstrated successfully in a novel segmented linear ion trap. The enhanced performance is enabled by incorporating the entire range of ion activation methods into a single platform in a highly dynamic fashion. The ion activation network comprises external injection of reagent ions, radical neutral species, photons, electrons, and collisions with neutrals. Axial segmentation of the two-dimensional trapping field provides access to a unique functionality landscape through a system of purpose-designed regions for processing ions with maximum flexibility. Design aspects of the segmented linear ion trap, termed the Omnitrap platform, are highlighted, and motion of ions trapped by rectangular waveforms is investigated experimentally by mapping the stability diagram, tracing secular frequencies, and exploring different isolation techniques. All fragmentation methods incorporated in the Omnitrap platform involving radical chemistry are shown to provide complete sequence coverage for partially unfolded ubiquitin. Three-stage (MS3) tandem mass spectrometry experiments combining collision-induced dissociation of radical ions produced by electron meta-ionization and further involving two intermediate steps of ion isolation and accumulation are performed with high efficiency, producing information rich spectra with signal-to-noise levels comparable to those obtained in a two-stage (MS2) experiment. The advanced capabilities of the Omnitrap platform to provide in-depth top-down MSn characterization of proteins are portrayed. Performance is further enhanced by connecting the Omnitrap platform to an Orbitrap mass analyzer, while successful integration with time-of-flight analyzers has already been demonstrated.
Collapse
Affiliation(s)
- Dimitris Papanastasiou
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Diamantis Kounadis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Alexandros Lekkas
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Ioannis Orfanopoulos
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Andreas Mpozatzidis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Athanasios Smyrnakis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Elias Panagiotopoulos
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Mariangela Kosmopoulou
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | | | - Kyle Fort
- Thermo
Fisher Scientific, Hanna-Kunath-Straße
11, 28199 Bremen, Germany
| | - Alexander Makarov
- Thermo
Fisher Scientific, Hanna-Kunath-Straße
11, 28199 Bremen, Germany
| | - Roman A. Zubarev
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17165 Solna, Sweden
| |
Collapse
|
8
|
Du M, Zhang K, Jiao L, Xu Y, Kong X. Differentiation of disaccharide isomers via a combination of IR and UV photodissociation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9218. [PMID: 34740281 DOI: 10.1002/rcm.9218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
RATIONALE The challenge of glycan identification due to their structural complexity and diversity has profited enormously from recent developments in mass spectrometry (MS)-related methods. For photodissociation MS, infrared (IR) and ultraviolet (UV) lasers can generate complementary fragment ions, so an effective combination of the two methods may provide rich and valuable fragmentation patterns for glycan analysis. METHODS A 7.0 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer equipped with a double-beam laser system was applied for the experiments. 3,5-Diiodo-L-tyrosine was selected as the assistant molecule to form complex ions with ten isomeric disaccharides through electrospray ionization. The complex ions were further isolated and irradiated by IR and UV lasers separately or continuously in the FTICR cell. RESULTS By combining the two complementary fragment spectra generated from the IR and UV lasers, a clear identification of all the ten isomers was achieved using their binary codes based on their fragmentation patterns. The double-beam method simplifies the experiment by introducing the two lasers sequentially in one experiment, providing richer fragmentation patterns and making the full discrimination easier. CONCLUSIONS This study demonstrates the capabilities of the combination of IR and UV photodissociation MS in the identification of diverse glycan isomers. The double-beam photodissociation method described here distinguished compositional, configurational and connectivity disaccharide isomers successfully. Compared with the data accumulation method based on separate IR and UV experiments, this method is simpler, faster, more flexible and also characterized by richer fragmentation patterns.
Collapse
Affiliation(s)
- Mengying Du
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Kailin Zhang
- Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin, China
| | - Luyang Jiao
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Yicheng Xu
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, China
| |
Collapse
|
9
|
Becher S, Wang H, Leeming MG, Donald WA, Heiles S. Influence of protein ion charge state on 213 nm top-down UVPD. Analyst 2021; 146:3977-3987. [PMID: 34009215 DOI: 10.1039/d1an00571e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultraviolet photodissociation (UVPD) is a powerful and rapidly developing method in top-down proteomics. Sequence coverages can exceed those obtained with collision- and electron-induced fragmentation methods. Because of the recent interest in UVPD, factors that influence protein fragmentation and sequence coverage are actively debated in the literature. Here, we performed top-down 213 nm UVPD experiments on a 7 T Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for the model proteins ubiquitin, myoglobin and cytochrome c that were electrosprayed from native, denaturing and supercharging solutions in order to investigate the effect of protein charge states on UVPD fragments. By performing UVPD in ultrahigh vacuum, factors associated with collisional cooling and any ion activation during transfer between mass analyzers can be largely eliminated. Sequence coverage increased from <10% for low charge states to >60% for high charge states for all three proteins. This trend is influenced by the overall charge state, i.e., charges per number of amino acid residues, and to a lesser degree by associated structural changes of protein ions of different charge states based on comparisons to published collision-cross section measurements. To rationalize this finding, and correlate sequence ion formation and identity with the number and location of protons, UVPD results were compared to protonation sites predicted based on electrostatic modelling. Assuming confined protonation sites, these results indicate the presence of two general fragmentation types; i.e., charge remote and charge directed. For moderately high protein charge states, fragment ions mostly originate in regions between likely protonation sites (charge remote), whereas sequence ions of highly charge protein ions occur either near backbone amide protonation sites at low-basicity residues (charge directed) or at charge remote sites (i.e., high-basicity residues). Overall, our results suggest that top-down 213 UVPD performance in the zero-pressure limit depends strongly on protein charge states and protonation sites can influence the location of backbone cleavages.
Collapse
Affiliation(s)
- Simon Becher
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
| | - Huixin Wang
- Mark Wainwright Analytical Centre, University of New South Wales, New South Wales, Australia
| | - Michael G Leeming
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
| |
Collapse
|
10
|
Kolbowski L, Belsom A, Rappsilber J. Ultraviolet Photodissociation of Tryptic Peptide Backbones at 213 nm. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1282-1290. [PMID: 32352297 PMCID: PMC7273743 DOI: 10.1021/jasms.0c00106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 05/23/2023]
Abstract
We analyzed the backbone fragmentation behavior of tryptic peptides of a four-protein mixture and of E. coli lysate subjected to ultraviolet photodissociation (UVPD) at 213 nm on a commercially available UVPD-equipped tribrid mass spectrometer. We obtained 15 178 unique high-confidence peptide UVPD spectrum matches by recording a reference beam-type collision-induced dissociation (HCD) spectrum of each precursor, ensuring that our investigation includes a broad selection of peptides, including those that fragmented poorly by UVPD. Type a, b, and y ions were most prominent in UVPD spectra, and median sequence coverage ranged from 5.8% (at 5 ms laser excitation time) to 45.0% (at 100 ms). Overall, the sequence fragment intensity remained relatively low (median: 0.4% (5 ms) to 16.8% (100 ms) of total intensity), and the remaining precursor intensity, high. The sequence coverage and sequence fragment intensity ratio correlated with the precursor charge density, suggesting that UVPD at 213 nm may suffer from newly formed fragments sticking together due to noncovalent interactions. The UVPD fragmentation efficiency therefore might benefit from supplemental activation, as was shown for ETD. Aromatic amino acids, most prominently tryptophan, facilitated UVPD. This points to aromatic tags as possible enhancers of UVPD. Data are available via ProteomeXchange with identifier PXD018176 and on spectrumviewer.org/db/UVPD-213nm-trypPep.
Collapse
Affiliation(s)
- Lars Kolbowski
- Bioanalytics, Institute of Biotechnology, Technische
Universität Berlin, 13355 Berlin, Germany
- Wellcome Centre for Cell Biology, School of Biological Sciences,
University of Edinburgh, Edinburgh EH9 3BF, United
Kingdom
| | - Adam Belsom
- Bioanalytics, Institute of Biotechnology, Technische
Universität Berlin, 13355 Berlin, Germany
- Wellcome Centre for Cell Biology, School of Biological Sciences,
University of Edinburgh, Edinburgh EH9 3BF, United
Kingdom
| | | |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Polasky DA, Dixit SM, Keating MF, Gadkari VV, Andrews PC, Ruotolo BT. Pervasive Charge Solvation Permeates Native-like Protein Ions and Dramatically Influences Top-down Sequencing Data. J Am Chem Soc 2020; 142:6750-6760. [DOI: 10.1021/jacs.0c01076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sugyan M. Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Michael F. Keating
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Philip C. Andrews
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
13
|
Fornelli L, Srzentić K, Toby TK, Doubleday PF, Huguet R, Mullen C, Melani RD, Dos Santos Seckler H, DeHart CJ, Weisbrod CR, Durbin KR, Greer JB, Early BP, Fellers RT, Zabrouskov V, Thomas PM, Compton PD, Kelleher NL. Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics. Mol Cell Proteomics 2020; 19:405-420. [PMID: 31888965 PMCID: PMC7000117 DOI: 10.1074/mcp.tir119.001638] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/29/2019] [Indexed: 11/06/2022] Open
Abstract
Top-down proteomics studies intact proteoform mixtures and offers important advantages over more common bottom-up proteomics technologies, as it avoids the protein inference problem. However, achieving complete molecular characterization of investigated proteoforms using existing technologies remains a fundamental challenge for top-down proteomics. Here, we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. Notably, the described UVPD setup applies multiple laser pulses to induce ion dissociation, and this feature can be used to optimize the fragmentation outcome based on the molecular weight of the analyzed biomolecule. When applied to complex proteoform mixtures in high-throughput top-down proteomics, 213 nm UVPD demonstrated a high degree of complementarity with the most employed fragmentation method in proteomics studies, higher-energy collisional dissociation (HCD). UVPD at 213 nm offered higher average proteoform sequence coverage and degree of proteoform characterization (including localization of post-translational modifications) than HCD. However, previous studies have shown limitations in applying database search strategies developed for HCD fragmentation to UVPD spectra which contains up to nine fragment ion types. We therefore performed an analysis of the different UVPD product ion type frequencies. From these data, we developed an ad hoc fragment matching strategy and determined the influence of each possible ion type on search outcomes. By paring down the number of ion types considered in high-throughput UVPD searches from all types down to the four most abundant, we were ultimately able to achieve deeper proteome characterization with UVPD. Lastly, our detailed product ion analysis also revealed UVPD cleavage propensities and determined the presence of a product ion produced specifically by 213 nm photons. All together, these observations could be used to better elucidate UVPD dissociation mechanisms and improve the utility of the technique for proteomic applications.
Collapse
Affiliation(s)
- Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Kristina Srzentić
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Timothy K Toby
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Peter F Doubleday
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134
| | | | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Henrique Dos Santos Seckler
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Caroline J DeHart
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | | | - Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208; Proteinaceous Inc., Evanston, Illinois 60201
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Bryan P Early
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | | | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208.
| |
Collapse
|
14
|
Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
15
|
Maitre P, Scuderi D, Corinti D, Chiavarino B, Crestoni ME, Fornarini S. Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications. Chem Rev 2019; 120:3261-3295. [PMID: 31809038 DOI: 10.1021/acs.chemrev.9b00395] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.
Collapse
Affiliation(s)
- Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| |
Collapse
|
16
|
Danquah BD, Röwer C, Opuni KM, El-Kased R, Frommholz D, Illges H, Koy C, Glocker MO. Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE). Mol Cell Proteomics 2019; 18:1543-1555. [PMID: 31147491 PMCID: PMC6683010 DOI: 10.1074/mcp.ra119.001429] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Epitope mapping, which is the identification of antigenic determinants, is essential for the design of novel antibody-based therapeutics and diagnostic tools. ITEM-THREE is a mass spectrometry-based epitope mapping method that can identify epitopes on antigens upon generating an immune complex in electrospray-compatible solutions by adding an antibody of interest to a mixture of peptides from which at least one holds the antibody's epitope. This mixture is nano-electrosprayed without purification. Identification of the epitope peptide is performed within a mass spectrometer that provides an ion mobility cell sandwiched in-between two collision cells and where this ion manipulation setup is flanked by a quadrupole mass analyzer on one side and a time-of-flight mass analyzer on the other side. In a stepwise fashion, immune-complex ions are separated from unbound peptide ions and dissociated to release epitope peptide ions. Immune complex-released peptide ions are separated from antibody ions and fragmented by collision induced dissociation. Epitope-containing peptide fragment ions are recorded, and mass lists are submitted to unsupervised data base search thereby retrieving both, the amino acid sequence of the epitope peptide and the originating antigen. ITEM-THREE was developed with antiTRIM21 and antiRA33 antibodies for which the epitopes were known, subjecting them to mixtures of synthetic peptides of which one contained the respective epitope. ITEM-THREE was then successfully tested with an enzymatic digest of His-tagged recombinant human β-actin and an antiHis-tag antibody, as well as with an enzymatic digest of recombinant human TNFα and an antiTNFα antibody whose epitope was previously unknown.
Collapse
Affiliation(s)
- Bright D Danquah
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Claudia Röwer
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | - Reham El-Kased
- ¶Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - David Frommholz
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany
| | - Harald Illges
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany;; **University of Applied Sciences Bonn-Rhein-Sieg, Institute for Functional Gene Analytics, Rheinbach, Germany
| | - Cornelia Koy
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Michael O Glocker
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Compagnon I, Schindler B, Renois-Predelus G, Daniel R. Lasers and ion mobility: new additions to the glycosaminoglycanomics toolkit. Curr Opin Struct Biol 2018; 50:171-180. [PMID: 30005299 DOI: 10.1016/j.sbi.2018.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022]
Abstract
Glycosaminoglycans are biopolymers present in mammalian cells or in the extracellular matrix. To address their structure, the nature of the hexuronic acids and the position of sulfate groups must be determined. Tandem mass spectrometry using collision induced dissociation or electron-based fragmentation techniques, is a well-established approach for the identification of glycans but suffers from the frequent lack of diagnostic fragments in the case of glycosaminoglycans. This review presents alternative fragmentation techniques, namely photofragmentation in the IR and the UV ranges. Alternative approaches based on the direct analysis of the molecular structure, including ion mobility spectrometry and ion spectroscopies are reviewed. The potential of future multidimensional workflows for glycosaminoglycanomics is discussed.
Collapse
Affiliation(s)
- Isabelle Compagnon
- Institut Universitaire de France IUF, 103 Boulevard St Michel, Paris F-75005, France; Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Baptiste Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Gina Renois-Predelus
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Régis Daniel
- Université Paris-Saclay, CNRS, CEA, Univ Evry, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, F-91025 Evry, France
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Scheffler K, Viner R, Damoc E. High resolution top-down experimental strategies on the Orbitrap platform. J Proteomics 2018; 175:42-55. [DOI: 10.1016/j.jprot.2017.03.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/08/2017] [Accepted: 03/31/2017] [Indexed: 10/19/2022]
|
21
|
Halim MA, MacAleese L, Lemoine J, Antoine R, Dugourd P, Girod M. Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:270-283. [PMID: 28980177 DOI: 10.1007/s13361-017-1794-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Mohammad A Halim
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Luke MacAleese
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
| | - Rodolphe Antoine
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France.
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
| |
Collapse
|
22
|
Becher S, Spengler B, Heiles S. Effects of wavelength, fluence, and dose on fragmentation pathways and photoproduct ion yield in 213 nm and 266 nm ultraviolet photodissociation experiments. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2018; 24:54-65. [PMID: 29141443 DOI: 10.1177/1469066717741747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultraviolet photodissociation tandem mass spectrometry is a powerful tool to investigate the structure of biomolecules, due to its ability to generate rich fragmentation patterns or bond selective cleavage, as a function of used laser wavelength, laser fluence, dose (number of accumulated laser pulses), and available chromophores. Herein, we report first results obtained with a newly developed two-wavelength (266 nm and 213 nm) ultraviolet photodissociation setup coupled to a Fourier-transform ion cyclotron resonance mass spectrometer. Photoproduct yields for protonated 3-iodo-l-tyrosine were up to ∼75%. Dose and fluence dependent measurements for protonated 3-iodo-l-tyrosine, doubly charged protonated bradykinin and Fe(II) attached to 1,2-dioleoyl-sn-glycero-3-phosphocholine reveal that the ultraviolet photodissociation mechanism for photoproduct formation qualitatively differs between these model systems. Three derived photodissociation models were used to interpret the experimental results and show that while protonated 3-iodo-l-tyrosine and Fe(II) attached to 1,2-dioleoyl-sn-glycero-3-phosphocholine most likely dissociates via a single-photon process, fragmentation of doubly charged bradykinin ions was found to be most consistent with sequential two-photon dissociation (213 nm). The introduced dissociation models present an easy means to study the mechanism of ultraviolet photodissociation processes for a variety of analytes without prior knowledge of their photochemistry or to optimize experimental conditions by adjusting laser fluence or number of laser pulses.
Collapse
Affiliation(s)
- Simon Becher
- 426460 Institute of Inorganic and Analytical Chemistry, Justus Liebig University , Giessen, Germany
| | - Bernhard Spengler
- 426460 Institute of Inorganic and Analytical Chemistry, Justus Liebig University , Giessen, Germany
| | - Sven Heiles
- 426460 Institute of Inorganic and Analytical Chemistry, Justus Liebig University , Giessen, Germany
| |
Collapse
|
23
|
Qi L, Ruck C, Spychalski G, King B, Wu B, Zhao Y. Writing Wrinkles on Poly(dimethylsiloxane) (PDMS) by Surface Oxidation with a CO 2 Laser Engraver. ACS APPLIED MATERIALS & INTERFACES 2018; 10:4295-4304. [PMID: 29302968 DOI: 10.1021/acsami.7b17622] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Surface wrinkles formed by the buckling of a strained stiff layer attached to a soft elastomer foundation have been widely used in a variety of applications. Micropatterning of wrinkled topographies is, however, limited by process/system complexities. In this article, we report an approach to write surface wrinkles with desired pattern geometries on poly(dimethylsiloxane) (PDMS) elastomers using a commercial infrared laser engraver with a spot size of 127 μm. Wrinkled micropatterns with wavelength from <50 to >300 μm were obtained in minutes without using special facilities or atmospheres. The minimal achievable pattern sizes of one-dimensional and two-dimensional patterns and the change of the minimal achievable pattern size with wrinkle orientation were investigated under a given set of operating parameters. Sub-spot size patterning was also demonstrated. To reduce surface cracking, a typical problem in large-area wrinkle patterning, a patterning scheme that separates neighboring laser exposure areas by nonexposure gaps was developed. In addition, micropatterns with gradient wrinkles were created on the surface. This is the first report that patterns microscale surface wrinkles on elastomer surfaces using infrared laser irradiation. The simple and versatile approach is expected to provide a fast yet controllable way to create wrinkled micropatterns at low cost to facilitate a broad array of studies in surface engineering, cellular biomechanics, and optics.
Collapse
Affiliation(s)
- Lin Qi
- Laboratory for Biomedical Microsystems, Department of Biomedical Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Cody Ruck
- Laboratory for Biomedical Microsystems, Department of Biomedical Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Griffin Spychalski
- Laboratory for Biomedical Microsystems, Department of Biomedical Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Brian King
- Laboratory for Biomedical Microsystems, Department of Biomedical Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Benxin Wu
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Yi Zhao
- Laboratory for Biomedical Microsystems, Department of Biomedical Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| |
Collapse
|
24
|
R Julian R. The Mechanism Behind Top-Down UVPD Experiments: Making Sense of Apparent Contradictions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1823-1826. [PMID: 28702929 PMCID: PMC5711567 DOI: 10.1007/s13361-017-1721-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 05/21/2023]
Abstract
Top-down ultraviolet photodissociation (UVPD) allows greater sequence coverage than any other currently available method, often fracturing the vast majority of peptide bonds in whole proteins. At the same time, UVPD can be used to dissociate noncovalent complexes assembled from multiple proteins without breaking any covalent bonds. Although the utility of these experiments is unquestioned, the mechanism underlying these seemingly contradictory results has been the subject of many discussions. Herein, some fundamental considerations of photochemistry are briefly summarized within the context of a proposed mechanism that rationalizes the experimental results obtained by UVPD. Considerations for future instrument design, in terms of wavelength choice and power, are briefly discussed. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
| |
Collapse
|
25
|
Chen J, Luo Z, Fu H, Yao J. Photoreactions of Porphyrins Initiated by Deep Ultraviolet Single Photons. J Phys Chem A 2017; 121:4626-4632. [DOI: 10.1021/acs.jpca.7b03635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Chen
- State Key Laboratory
for
Structural Chemistry of Unstable and Stable species, and Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhixun Luo
- State Key Laboratory
for
Structural Chemistry of Unstable and Stable species, and Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongbing Fu
- State Key Laboratory
for
Structural Chemistry of Unstable and Stable species, and Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiannian Yao
- State Key Laboratory
for
Structural Chemistry of Unstable and Stable species, and Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Fagerquist CK. Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization. Expert Rev Proteomics 2016; 14:97-107. [DOI: 10.1080/14789450.2017.1260451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clifton K. Fagerquist
- United States Department of Agriculture (USDA), Agricultural Research Service, Albany, CA, USA
| |
Collapse
|
28
|
Egorov D, Schwob L, Lalande M, Hoekstra R, Schlathölter T. Near edge X-ray absorption mass spectrometry of gas phase proteins: the influence of protein size. Phys Chem Chem Phys 2016; 18:26213-26223. [DOI: 10.1039/c6cp05254a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The response of gas-phase proteins upon soft X-ray absorption depends strongly on the proteins size.
Collapse
Affiliation(s)
- D. Egorov
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- Netherlands
| | - L. Schwob
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - M. Lalande
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - R. Hoekstra
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- Netherlands
| | - T. Schlathölter
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- Netherlands
| |
Collapse
|