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DeFiglia SA, Szot CW, Håkansson K. Negative-Ion Electron Capture Dissociation of MALDI-Generated Peptide Anions. Anal Chem 2024; 96:8800-8806. [PMID: 38742421 DOI: 10.1021/acs.analchem.4c01292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Negative-ion electron capture dissociation (niECD) is an anion MS/MS technique that provides fragmentation analogous to conventional ECD, including high peptide sequence coverage and retention of labile post-translational modifications (PTMs). niECD has been proposed to be the most efficient for salt-bridged zwitterionic precursor ion structures. Several important PTMs, e.g., sulfation and phosphorylation, are acidic and can, therefore, be challenging to characterize in the positive-ion mode. Furthermore, PTM-friendly techniques, such as ECD, require multiple precursor ion-positive charges. By contrast, singly charged ions, refractory to ECD, are most compatible with niECD. Because electrospray ionization (ESI) typically yields multiply charged ions, we sought to explore matrix-assisted laser desorption/ionization (MALDI) in combination with niECD. However, the requirement for zwitterionic gaseous structures may preclude efficient niECD of MALDI-generated anions. Unexpectedly, we found that niECD of anions from MALDI is not only possible but proceeds with similar or higher efficiency compared with ESI-generated anions. Matrix selection did not appear to have a major effect. With MALDI, niECD is demonstrated up to m/z ∼4300. For such larger analytes, multiple electron captures are observed, resulting in triply charged fragments from singly charged precursor ions. Such charge-increased fragments show improved detectability. Furthermore, significantly improved (∼20-fold signal-to-noise increase) niECD spectral quality is achieved with equivalent sample amounts from MALDI vs ESI. Overall, the reported combination with MALDI significantly boosts the analytical utility of niECD.
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Affiliation(s)
- Steven A DeFiglia
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Carson W Szot
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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2
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Surface-sampling mass spectrometry to study proteins and protein complexes. Essays Biochem 2023; 67:229-241. [PMID: 36748325 PMCID: PMC10070487 DOI: 10.1042/ebc20220191] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/08/2023]
Abstract
This review aims to summarise the current capabilities of surface mass spectrometry (MS) approaches that offer intact protein analysis, and that of non-covalent complexes. Protein analysis is largely achieved via matrix-assisted laser desorption/ionisation (MALDI), which is in itself a surface analysis approach or solvent-based electrospray ionisation (ESI). Several surface sampling approaches have been developed based on ESI, and those that have been used for intact protein analysis will be discussed below. The extent of protein coverage, top-down elucidation, and probing of protein structure for native proteins and non-covalent complexes will be discussed for each approach. Strategies for improving protein analysis, ranging from sample preparation, and sampling methods to instrument modifications and the inclusion of ion mobility separation in the workflow will also be discussed. The relative benefits and drawbacks of each approach will be summarised, providing an overview of current capabilities.
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3
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Duarte PL, Andrade FRN, Sousa ARDO, Andrade AL, de Vasconcelos MA, Teixeira EH, Nagano CS, Sampaio AH, Carneiro RF. A fibrinogen-related Lectin from Echinometra lucunter represents a new FReP family in Echinodermata phylum. FISH & SHELLFISH IMMUNOLOGY 2022; 131:150-159. [PMID: 36216229 DOI: 10.1016/j.fsi.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Fibrinogen-related proteins (FREPs) have been identified in several animals. They are involved in the body's defense, acting as mediators of phagocytosis. Ficolins and intelectins are some of the most studied Fibrinogen-related Domain (FReD)-containing lectins. In this work, we have isolated a singular FReD-containing lectin, which cannot be classified as ficolin or intelectin. ELL (Echinometra lucunter lectin) was isolated from coelomic plasma by affinity chromatography on xanthan gum. Primary structure was determined by tandem mass spectrometry. Moreover, antimicrobial activity of ELL was evaluated against planktonic cells and biofilm of Escherichia coli, Staphylococcus aureus and S. epidermidis. ELL showed hemagglutinating activity in Ca2+ presence, which was inhibited by glycoprotein mucin and thyroglobulin. Complete amino acid sequence consisted of 229 residues, including a FReD in the N-terminal. Searches for similarity found that ELL was very close to putative proteins from Strongylocentrotus purpuratus. ELL showed moderate similarity with uncharacterized sea stars proteins and protochordate intelectins. ELL was able to inhibit the planktonic growth of the Gram-positive bacteria and significantly reduce the biofilm formation of all bacteria tested. In conclusion, we identified a new type of FReP-containing lectin with some structural and functional conservation towards intelectins.
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Affiliation(s)
- Philippe Lima Duarte
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Francisco Regivânio Nascimento Andrade
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Andressa Rocha de Oliveira Sousa
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Alexandre Lopes Andrade
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil
| | - Mayron Alves de Vasconcelos
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil; Laboratorio de Quimica de Proteínas e Produtos Naturais - LABQUIMP, Universidade do Estado de Minas Gerais, Unidade Divinópolis, 35501-170, Divinópolis, Minas Gerais, Brazil
| | - Edson Holanda Teixeira
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil
| | - Celso Shiniti Nagano
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Alexandre Holanda Sampaio
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Rômulo Farias Carneiro
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil.
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4
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Kitashoji A, Kitagawa K, Fujihara A, Yatsuhashi T. Charge Transfer and Metastable Ion Dissociation of Multiply Charged Molecular Cations Observed by Using Reflectron Time-of-Flight Mass Spectrometry. Chemphyschem 2020; 21:847-852. [PMID: 32096267 DOI: 10.1002/cphc.202000021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/23/2020] [Indexed: 11/07/2022]
Abstract
A multiply charged molecule expands the range of a mass window and is utilized as a precursor to provide rich sequence coverage; however, reflectron time-of-flight mass spectrometer has not been well applied to the product ion analysis of multiply charged precursor ions. Here, we demonstrate that the range of the mass-to-charge ratio of measurable product ions is limited in the cases of multiply charged precursor ions. We choose C6 F6 as a model molecule to investigate the reactions of multiply charged molecular cations formed in intense femtosecond laser fields. Measurements of the time-of-flight spectrum of C6 F6 by changing the potential applied to the reflectron, combined with simulation of the ion trajectory, can identify the species detected behind the reflectron as the neutral species and/or ions formed by the collisional charge transfer. Moreover, the metastable ion dissociations of doubly and triply charged C6 F6 are identified. The detection of product ions in this manner can diminish interference by the precursor ion. Moreover, it does not need precursor ion separation before product ion analysis. These advantages would expand the capability of mass spectrometry to obtain information about metastable ion dissociation of multiply charged species.
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Affiliation(s)
- Akihiro Kitashoji
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Kosei Kitagawa
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Akimasa Fujihara
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Tomoyuki Yatsuhashi
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
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5
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Curcio R, Aiello D, Vozza A, Muto L, Martello E, Cappello AR, Capobianco L, Fiermonte G, Siciliano C, Napoli A, Dolce V. Cloning, Purification, and Characterization of the Catalytic C-Terminal Domain of the Human 3-Hydroxy-3-methyl glutaryl-CoA Reductase: An Effective, Fast, and Easy Method for Testing Hypocholesterolemic Compounds. Mol Biotechnol 2019; 62:119-131. [DOI: 10.1007/s12033-019-00230-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Zhan L, Liu Y, Xie X, Xiong C, Nie Z. Heat-Induced Rearrangement of the Disulfide Bond of Lactoglobulin Characterized by Multiply Charged MALDI-TOF/TOF Mass Spectrometry. Anal Chem 2018; 90:10670-10675. [DOI: 10.1021/acs.analchem.8b02563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Lingpeng Zhan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liu
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaobo Xie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- National Center for Mass Spectrometry in Beijing, Beijing 100190, China
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7
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Lou X, Li B, de Waal BFM, Schill J, Baker MB, Bovee RAA, van Dongen JLJ, Milroy LG, Meijer EW. Fragmentation of organic ions bearing fixed multiple charges observed in MALDI MS. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:39-47. [PMID: 28963745 DOI: 10.1002/jms.4035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/11/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) was used to analyze a series of synthetic organic ions bearing fixed multiple charges. Despite the multiple intrinsic charges, only singly charged ions were recorded in each case. In addition to the pseudo-molecular ions formed by counterion adduction, deprotonation and electron capture, a number of fragment ions were also observed. Charge splitting by fragmentation was found to be a viable route for charge reduction leading to the formation of the observed singly charged fragment ions. Unlike multivalent metal ions, organic ions can rearrange and/or fragment during charge reduction. This fragmentation process will evidently complicate the interpretation of the MALDI MS spectrum. Because MALDI MS is usually considered as a soft ionization technique, the fragment ion peaks can easily be erroneously interpreted as impurities. Therefore, the awareness and understanding of the underlying MALDI-induced fragmentation pathways is essential for a proper interpretation of the corresponding mass spectra. Due to the fragment ions generated during charge reduction, special care should be taken in the MALDI MS analysis of multiply charged ions. In this work, the possible mechanisms by which the organic ions bearing fixed multiple charges fragment are investigated. With an improved understanding of the fragmentation mechanisms, MALDI TOF MS should still be a useful technique for the characterization of organic ions with fixed multiple charges.
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Affiliation(s)
- Xianwen Lou
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Bao Li
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Bas F M de Waal
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Jurgen Schill
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Matthew B Baker
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Ralf A A Bovee
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Joost L J van Dongen
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - E W Meijer
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
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8
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Chen B, Lietz CB, OuYang C, Zhong X, Xu M, Li L. Matrix-assisted ionization vacuum for protein detection, fragmentation and PTM analysis on a high resolution linear ion trap-orbitrap platform. Anal Chim Acta 2016; 916:52-9. [PMID: 27016438 DOI: 10.1016/j.aca.2016.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/12/2016] [Indexed: 11/28/2022]
Abstract
Matrix-assisted ionization vacuum (MAIV) is a novel ionization technique that generates multiply charged ions in vacuum without the use of laser ablation or high voltage. MAIV can be achieved in intermediate-vacuum and high-vacuum matrix-assisted laser desorption/ionization (MALDI) sources and electrospray ionization (ESI) sources without instrument modification. Herein, we adapt MAIV onto the MALDI-LTQ-Orbitrap XL platform for biomolecule analysis. As an attractive alternative to MALDI for in solution and in situ analysis of biomolecules, MAIV coupling to high resolution and accurate mass (HRAM) MS instrument has successfully expanded the mass detection range and improved the fragmentation efficiency due to the generation of multiply charged ions. Additionally, the softness of MAIV enables potential application in labile post-translational modification (PTM) analysis. In this study, proteins as large as 18.7 kDa were detected with up to 18 charges; intact peptides with labile PTM were well preserved during the ionization process and characterized MS/MS; peptides and proteins in complex tissue samples were detected and identified both in liquid extracts and in situ. Moreover, we demonstrated that this method facilitates MS/MS analysis with improved fragmentation efficiency compared to MALDI-MS/MS.
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Affiliation(s)
- Bingming Chen
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Christopher B Lietz
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Chuanzi OuYang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Meng Xu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States; Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, United States.
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9
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Ryumin P, Brown J, Morris M, Cramer R. Investigation and optimization of parameters affecting the multiply charged ion yield in AP-MALDI MS. Methods 2016; 104:11-20. [PMID: 26827934 DOI: 10.1016/j.ymeth.2016.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 10/22/2022] Open
Abstract
Liquid matrix-assisted laser desorption/ionization (MALDI) allows the generation of predominantly multiply charged ions in atmospheric pressure (AP) MALDI ion sources for mass spectrometry (MS) analysis. The charge state distribution of the generated ions and the efficiency of the ion source in generating such ions crucially depend on the desolvation regime of the MALDI plume after desorption in the AP-to-vacuum inlet. Both high temperature and a flow regime with increased residence time of the desorbed plume in the desolvation region promote the generation of multiply charged ions. Without such measures the application of an electric ion extraction field significantly increases the ion signal intensity of singly charged species while the detection of multiply charged species is less dependent on the extraction field. In general, optimization of high temperature application facilitates the predominant formation and detection of multiply charged compared to singly charged ion species. In this study an experimental set-up and optimization strategy is described for liquid AP-MALDI MS which improves the ionization efficiency of selected ion species up to 14 times. In combination with ion mobility separation, the method allows the detection of multiply charged peptide and protein ions for analyte solution concentrations as low as 2fmol/μL (0.5μL, i.e. 1fmol, deposited on the target) with very low sample consumption in the low nL-range.
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Affiliation(s)
- Pavel Ryumin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Jeffery Brown
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK; Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, UK
| | - Michael Morris
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.
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10
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Recent methodological advances in MALDI mass spectrometry. Anal Bioanal Chem 2014; 406:2261-78. [PMID: 24652146 DOI: 10.1007/s00216-014-7646-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/17/2014] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is widely used for characterization of large, thermally labile biomolecules. Advantages of this analytical technique are high sensitivity, robustness, high-throughput capacity, and applicability to a wide range of compound classes. For some years, MALDI-MS has also been increasingly used for mass spectrometric imaging as well as in other areas of clinical research. Recently, several new concepts have been presented that have the potential to further advance the performance characteristics of MALDI. Among these innovations are novel matrices with low proton affinities for particularly efficient protonation of analyte molecules, use of wavelength-tunable lasers to achieve optimum excitation conditions, and use of liquid matrices for improved quantification. Instrumental modifications have also made possible MALDI-MS imaging with cellular resolution as well as an efficient generation of multiply charged MALDI ions by use of heated vacuum interfaces. This article reviews these recent innovations and gives the author's personal outlook of possible future developments.
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Lin Y, Yin Z, Wang X, Li W, Hang W. Role of three-body recombination for charge reduction in MALDI process. Analyst 2013; 138:2964-9. [DOI: 10.1039/c3an36749e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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Soltwisch J, Jaskolla TW, Hillenkamp F, Karas M, Dreisewerd K. Ion Yields in UV-MALDI Mass Spectrometry As a Function of Excitation Laser Wavelength and Optical and Physico-Chemical Properties of Classical and Halogen-Substituted MALDI Matrixes. Anal Chem 2012; 84:6567-76. [DOI: 10.1021/ac3008434] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens Soltwisch
- Institute of Medical Physics
and Biophysics, University of Münster, Robert-Koch-Strasse 31, 48149 Münster, Germany
| | - Thorsten W. Jaskolla
- Institute of Medical Physics
and Biophysics, University of Münster, Robert-Koch-Strasse 31, 48149 Münster, Germany
- Cluster of Excellence Macromolecular
Complexes, Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt,
Germany
| | - Franz Hillenkamp
- Institute of Medical Physics
and Biophysics, University of Münster, Robert-Koch-Strasse 31, 48149 Münster, Germany
| | - Michael Karas
- Cluster of Excellence Macromolecular
Complexes, Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt,
Germany
| | - Klaus Dreisewerd
- Institute of Medical Physics
and Biophysics, University of Münster, Robert-Koch-Strasse 31, 48149 Münster, Germany
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13
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The study of interferences for diagnosing albuminuria by matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. Clin Chim Acta 2012; 413:875-82. [DOI: 10.1016/j.cca.2012.01.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/20/2022]
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14
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Mädler S, Barylyuk K, Boeri Erba E, Nieckarz RJ, Zenobi R. Compelling advantages of negative ion mode detection in high-mass MALDI-MS for homomeric protein complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:213-224. [PMID: 22131225 DOI: 10.1007/s13361-011-0274-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/04/2011] [Accepted: 10/08/2011] [Indexed: 05/31/2023]
Abstract
Chemical cross-linking in combination with high-mass MALDI mass spectrometry allows for the rapid identification of interactions and determination of the complex stoichiometry of noncovalent protein-protein interactions. As the molecular weight of these complexes increases, the fraction of multiply charged species typically increases. In the case of homomeric complexes, signals from multiply charged multimers overlap with singly charged subunits. Remarkably, spectra recorded in negative ion mode show lower abundances of multiply charged species, lower background, higher reproducibility, and, thus, overall cleaner spectra compared with positive ion mode spectra. In this work, a dedicated high-mass detector was applied for measuring high-mass proteins (up to 200 kDa) by negative ion mode MALDI-MS. The influences of sample preparation and instrumental parameters were carefully investigated. Relative signal integrals of multiply charged anions were relatively independent of any of the examined parameters and could thus be approximated easily for the spectra of cross-linked complexes. For example, the fraction of doubly charged anions signals overlapping with the signals of singly charged subunits could be more precisely estimated than in positive ion mode. Sinapinic acid was found to be an excellent matrix for the analysis of proteins and cross-linked protein complexes in both ion modes. Our results suggest that negative ion mode data of chemically cross-linked protein complexes are complementary to positive ion mode data and can in some cases represent the solution phase situation better than positive ion mode.
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Affiliation(s)
- Stefanie Mädler
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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15
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Lin YH, Lee CC, Chang FR, Chang WH, Wu YC, Chang JG. 16-hydroxycleroda-3,13-dien-15,16-olide regulates the expression of histone-modifying enzymes PRC2 complex and induces apoptosis in CML K562 cells. Life Sci 2011; 89:886-95. [PMID: 21983300 DOI: 10.1016/j.lfs.2011.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 09/08/2011] [Accepted: 09/13/2011] [Indexed: 01/25/2023]
Abstract
AIMS Histone modifications play central epigenetic roles in regulating the entire genome of the cell and cell proliferation. Herein, we investigated the effects of the natural compound, 16-hydroxycleroda-3,13-dien-15,16-olide (PL3), on the expressions of histone-modifying enzymes, and examined how it induces apoptosis in leukemia K562 cells. MAIN METHODS Cell proliferation was determined by an MTT assay, and histone-modifying enzyme gene expressions were investigated by a quantitative real-time PCR. Protein expressions were analyzed by a Western blot analysis. The histone H3K27 distribution was observed with immunofluorescence staining. To verify polycomb repressive complex 2 (PRC2) complex downstream gene expressions, a gene-expression array was performed to determine gene regulations. KEY FINDINGS PL3 induced apoptosis and modulated many histone-modifying enzymes, especially the two PRC2 components, enhancer of zeste homolog 2 (EZH2) and suppressor of zeste 12 homolog (Suz12). Genes repressed by PRC2 were shown to be reactivated by PL3. Of these, 10 genes targeted by the PRC2 complex were identified, and expressions of 10 pro-/antiapoptotic genes were significantly regulated; these effects may have contributed to PL3-induced apoptosis in K562 cells. Regulation of other histone-modifying enzymes, including Aurora B, may also be involved in cell-cycle regulation. SIGNIFICANCE Our data suggest that the induction of apoptosis by PL3 might partly occur through both a reduction in PRC2-mediated gene silencing and the reactivation of downstream tumor suppressor gene expressions. PL3 acts as a novel small-molecule histone modulator, which can potentially contribute to cancer chemotherapy singly or as a combined medication.
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Affiliation(s)
- Yi-Hsiung Lin
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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16
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Lin YH, Lee CC, Chan WL, Chang WH, Wu YC, Chang JG. 16-Hydroxycleroda-3,13-dien-15,16-olide deregulates PI3K and Aurora B activities that involve in cancer cell apoptosis. Toxicology 2011; 285:72-80. [DOI: 10.1016/j.tox.2011.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 04/07/2011] [Accepted: 04/08/2011] [Indexed: 11/16/2022]
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17
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Abstract
The comprehensive analysis of intact proteins down to the level of their individual amino acid sequence and the entirety of post-translational modifications is an area that can hardly be covered by the typical workflow in MS based protein analysis, which comprises enzymatic digestion, mass spectrometric analysis and subsequent database search. This approach typically provides 20-80% sequence coverage, which is not sufficient for the characterization of biopharmaceuticals, for example. This generates the requirement for a comprehensive analysis of the protein, without the risk of losing sequence information due to undetected peptides. Top-down sequencing of proteins starts from the intact protein, typically by determining the intact protein mass in the first step, a fragmentation of the intact protein is then performed within the mass spectrometer, resulting in fragment ions that allow us to pinpoint the protein sequence, as well as potential modifications or mutations in their localization and structure. A number of technologies have been developed for this task in the last few years, based on various different mass spectrometric instrument configurations, but typically based on the same technology platforms as used for bottom-up strategies. Thus, the use of one specific instrument often allows the application of top-down and bottom-up technologies in a complementary way, providing much more detailed information about the proteins of interest than either of the approaches alone.
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18
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Lourantos E, Ramirez OM, Giannakopulos AE, Beran KA, Derrick PJ, Bashir S. The use of a silica-based heat sink to “uncouple” the matrix-assisted laser desorption/ionization (MALDI) mechanism. CAN J CHEM 2011. [DOI: 10.1139/v10-154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The relationships between ion yield(s) as a function of desorption alone and (or) ionization was investigated using two model systems. In the first model system, a carbohydrate (2,3,6-tri-O-methyl-β-cyclodextrin, TMBCD), which could be directly laser desorbed, was analyzed with and without a silicon-based heat sink compound (HSC). The HSC allowed heat to pass through but obstructed the flow of charge. In the second model system, a peptide (substance P), which ccould not be laser desorbed, was analyzed under similar conditions. The ion yield of TMBCD under either system of heat conductivity was similar, whereas the ion yield of the peptide with the heat sink was negligible. Compounds that are predominately cationized either in the gas phase or preformed in solution give an ion yield that is not dependent upon the surface conditions, whereas compounds that are not ordinarily cationized are affected by the emission of electrons from the metal surface.
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Affiliation(s)
- E. Lourantos
- Institute of Mass Spectrometry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physical Sciences, The University of Texas of the Permian Basin, 4901 E. University Blvd., Odessa, TX 79762, USA
| | - O. M. Ramirez
- Institute of Mass Spectrometry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physical Sciences, The University of Texas of the Permian Basin, 4901 E. University Blvd., Odessa, TX 79762, USA
| | - A. E. Giannakopulos
- Institute of Mass Spectrometry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physical Sciences, The University of Texas of the Permian Basin, 4901 E. University Blvd., Odessa, TX 79762, USA
| | - K. A. Beran
- Institute of Mass Spectrometry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physical Sciences, The University of Texas of the Permian Basin, 4901 E. University Blvd., Odessa, TX 79762, USA
| | - Peter J. Derrick
- Institute of Mass Spectrometry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physical Sciences, The University of Texas of the Permian Basin, 4901 E. University Blvd., Odessa, TX 79762, USA
| | - S. Bashir
- Institute of Mass Spectrometry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physical Sciences, The University of Texas of the Permian Basin, 4901 E. University Blvd., Odessa, TX 79762, USA
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19
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Ke Y, Kailasa SK, Wu HF, Nawaz M. Surface-modified TiO2 nanoparticles as affinity probes and as matrices for the rapid analysis of phosphopeptides and proteins in MALDI-TOF-MS. J Sep Sci 2010; 33:3400-8. [DOI: 10.1002/jssc.201000415] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Liu BH, Charkin OP, Klemenko N, Chen CW, Wang YS. Initial Ionization Reaction in Matrix-Assisted Laser Desorption/Ionization. J Phys Chem B 2010; 114:10853-9. [DOI: 10.1021/jp104178m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bo-Hong Liu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang District, Taipei 115, Taiwan, R. O. C., Institute of Problems of Chemical Physics, Russian Academy of Sciences, Institutskii pr. 18, Chernogolovka, Moscow oblast, 142432, Russia, and Lomonosov State Academy of Fine Chemical Technology, pr. Vernadskogo 86, Moscow, 117571, Russia
| | - Oleg P. Charkin
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang District, Taipei 115, Taiwan, R. O. C., Institute of Problems of Chemical Physics, Russian Academy of Sciences, Institutskii pr. 18, Chernogolovka, Moscow oblast, 142432, Russia, and Lomonosov State Academy of Fine Chemical Technology, pr. Vernadskogo 86, Moscow, 117571, Russia
| | - Nina Klemenko
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang District, Taipei 115, Taiwan, R. O. C., Institute of Problems of Chemical Physics, Russian Academy of Sciences, Institutskii pr. 18, Chernogolovka, Moscow oblast, 142432, Russia, and Lomonosov State Academy of Fine Chemical Technology, pr. Vernadskogo 86, Moscow, 117571, Russia
| | - Chiu Wen Chen
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang District, Taipei 115, Taiwan, R. O. C., Institute of Problems of Chemical Physics, Russian Academy of Sciences, Institutskii pr. 18, Chernogolovka, Moscow oblast, 142432, Russia, and Lomonosov State Academy of Fine Chemical Technology, pr. Vernadskogo 86, Moscow, 117571, Russia
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang District, Taipei 115, Taiwan, R. O. C., Institute of Problems of Chemical Physics, Russian Academy of Sciences, Institutskii pr. 18, Chernogolovka, Moscow oblast, 142432, Russia, and Lomonosov State Academy of Fine Chemical Technology, pr. Vernadskogo 86, Moscow, 117571, Russia
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21
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Abonnenc M, Qiao L, Liu B, Girault HH. Electrochemical aspects of electrospray and laser desorption/ionization for mass spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2010; 3:231-54. [PMID: 20636041 DOI: 10.1146/annurev.anchem.111808.073740] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Soft-ionization methods, namely electrospray ionization and laser desorption/ionization, are widely used to transfer large molecules as intact gas-phase ions either from a solution or from a solid substrate. During both processes, in-source electrochemical and photoelectrochemical reactions occur. These electrode reactions, which take place at interfaces, play important roles in influencing the ionization products, but they have received little attention. We show that having good control over both types of electrochemical reactions can lead to new analytical applications. Examples include online tagging by grafting of mass tags and in-source photooxidation of peptides.
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Affiliation(s)
- Mélanie Abonnenc
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Switzerland.
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22
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Liu BH, Lee YT, Wang YS. Incoherent production reactions of positive and negative ions in matrix-assisted laser desorption/ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1078-86. [PMID: 19299167 DOI: 10.1016/j.jasms.2009.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Revised: 02/02/2009] [Accepted: 02/03/2009] [Indexed: 05/08/2023]
Abstract
Utilizing synchronized dual-polarity matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, we found good evidence of the incoherent production of positive and negative matrix ions. Using thin, homogeneous 2,5-dehydroxybenzoic acid (DHB) matrix films, positive and negative matrix ions were found to appear at different threshold laser fluences. The presence of molecular matrix ions of single charge polarity suggests that the existence of DHB ion-pairs may not be a prerequisite in MALDI. Photoelectrons induced by the laser excitation may assist the production of negative DHB ions, as shown in experiments conducted with stainless steel and glass substrates. At high laser fluences, the relative yield of positive and negative matrix ions remained constant when homogeneous matrix films were used, but it fluctuated significantly with inhomogeneous crystal morphology. This result is also inconsistent with the hypothesis that matrix ion-pairs are essential primary ions. Evidence from both low and high laser fluences suggests that the productions of positive and negative matrix ions in MALDI may occur via independent pathways.
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Affiliation(s)
- Bo-Hong Liu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan ROC
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23
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Flosadóttir HD, Stano M, Ingólfsson O. Sodium controlled selective reactivity of protonated deoxy-oligonucleotides in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:689-696. [PMID: 19200751 DOI: 10.1016/j.jasms.2008.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 12/08/2008] [Accepted: 12/08/2008] [Indexed: 05/27/2023]
Abstract
Metastable fragmentation of the positively charged, hexameric oligonucleotides 5'-d(TTXYTT) (X and Y are dC, dG, or dA) and 5'-d(CTCGTT), 5'-d(TTCGTC) and 5'-d(CTCGTC) is studied after matrix assisted laser desorption/ionization (MALDI). The influence of the degree of sodiation, i.e., when the acidic protons are one by one exchanged against sodium ions, is systematically studied for the exchange of up to seven protons against sodium ions. Exchanging the acidic protons against sodium gradually quenches the backbone cleavage through the w and a-B channels, and quantitative quenching of these channels is generally achieved with the exchange of four protons against sodium ions. At the same time, the exchange of protons against sodium ions promotes the loss of a neutral, high proton affinity base. The formation of the w and a-B fragments is found to be highly dependent on the sequence of the central bases. A single mechanism consistent with these observations is proposed. In addition to the quenching of the classical w and a-B reaction channels, a drastic and abrupt on/off-switching of new reaction channels is observed as the degree of sodiation successively increases. These channels involve selective loss of the two central bases and the excision of a phosphodiester group and a sugar unit from the center of the oligonucleotides. Synchronously, the two terminal fragments recombine to form a tetramer containing the two terminal nucleosides from each end of the hexamer. Possible mechanism explaining these remarkable channels are discussed.
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24
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Liu Z, Schey KL. Fragmentation of multiply-charged intact protein ions using MALDI TOF-TOF mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:231-8. [PMID: 17693096 PMCID: PMC2288703 DOI: 10.1016/j.jasms.2007.06.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 05/23/2007] [Accepted: 06/15/2007] [Indexed: 05/12/2023]
Abstract
Top down proteomics in a TOF-TOF instrument was further explored by examining the fragmentation of multiply charged precursors ions generated by matrix-assisted laser desorption ionization. Evaluation of sample preparation conditions allowed selection of solvent/matrix conditions and sample deposition methods to produce sufficiently abundant doubly and triply charged precursor ions for subsequent CID experiments. As previously reported, preferential cleavage was observed at sites C-terminal to acidic residues and N-terminal to proline residues for all ions examined. An increase in nonpreferential fragmentation as well as additional low mass product ions was observed in the spectra from multiply charged precursor ions providing increased sequence coverage. This enhanced fragmentation from multiply charged precursor ions became increasingly important with increasing protein molecular weight and facilitates protein identification using database searching algorithms. The useable mass range for MALDI TOF-TOF analysis of intact proteins has been expanded to 18.2 kDa using this approach.
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Affiliation(s)
- Zhaoyang Liu
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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25
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Castellana ET, Russell DH. Tailoring nanoparticle surface chemistry to enhance laser desorption ionization of peptides and proteins. NANO LETTERS 2007; 7:3023-5. [PMID: 17887713 DOI: 10.1021/nl071469w] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Gold nanoparticles capped with 4-aminothiophenol have been employed for laser desorption ionization mass spectrometry of biomolecules. We demonstrate that the capped nanoparticles increase ion yields, decrease ion fragmentation, and increase the useful analyte mass range when compared to other nanoparticle systems. These results will allow for further development of nanoparticles with both targeting and enhanced ionization abilities to aid in biomarker screening.
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Affiliation(s)
- Edward T Castellana
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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26
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Ibáñez AJ, Muck A, Svatos A. Dissipation of charge on MALDI-TOF polymeric chips using an electron-acceptor: analysis of proteins. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:634-40. [PMID: 17370249 DOI: 10.1002/jms.1192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Disposable polymeric devices used for direct sample pretreatment/signal enhancement and MALDI-MS analyses of biomolecules suffer from the accumulation of electric charge and related positive mass shifts due to photoelectric effects on non-conductive surfaces after irradiation with lasers. The effects of surface charging on the mass shift of protein spectra during MALDI-TOF/MS measurements on copolymeric sample array chips were studied. Methyl viologen is used to monitor the development of charge and is demonstrated to be an effective electron scavenger. The use of such reducible species leads to increased accuracy, signal homogeneity, and resolution for mass spectral measurements of proteins in mixtures with sinapinic and 2,5-dihydroxybenzoic (DHB) acids. This approach can be used on a wide range of nonconductive support materials.
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Affiliation(s)
- Alfredo J Ibáñez
- Mass Spectrometry Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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27
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Knochenmuss R, McCombie G, Faderl M. Ion Yields of Thin MALDI Samples: Dependence on Matrix and Metal Substrate and Implications for Models. J Phys Chem A 2006; 110:12728-33. [PMID: 17125285 DOI: 10.1021/jp064760t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thin MALDI samples can perform differently than thicker samples, on metal substrates. Divergent results and models for the effect have been presented. Positive and negative yields are investigated here for three matrixes (2,5-dihydroxybenzoic acid (DHB), sinapinic acid, and alpha-cyano 4-hydroxycinnamic acid) on stainless steel and gold substrates. Samples were electrosprayed for uniformity and thickness control and imaged across a metal-metal boundary. Thin sample enhancement is found in both polarities for all three matrixes on a steel substrate. On gold, only alpha-cyano-4-hydroxycinnamic acid shows enhancement. These and earlier data are used to evaluate two models. The first is based on one-photon photoelectron emission from the metal; the second one, on two-photon matrix ionization at the metal interface. The surface-enhanced matrix photoionization model best fits the evidence, including the fluence dependence of electron emission from DHB on steel.
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Affiliation(s)
- R Knochenmuss
- Novartis Institutes of Biomedical Research, 4002 Basel, Switzerland.
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28
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Alves S, Fournier F, Afonso C, Wind F, Tabet JC. Gas-phase ionization/desolvation processes and their effect on protein charge state distribution under matrix-assisted laser desorption/ionization conditions. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2006; 12:369-83. [PMID: 17404427 DOI: 10.1255/ejms.822] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The charge state distribution of proteins was studied as a function of experimental conditions, to improve the understanding of the matrix-assisted laser desorption/ionization (MALDI) mechanisms. The relative abundances of the multiply-charged ions appear to be a function of the matrix chosen, the laser fluence and the matrix-to-analyte molar ratio. A correlation is found between the matrix proton affinity and the yield of singly- versus multiply-charged ions. These results are in good agreement with a model in which gas-phase intracluster reactions play a significant role in analyte ion formation. A new model for endothermic desolvation processes in ultraviolet/MALDI is presented and discussed. It is based upon the existence of highly-charged precursor clusters and, complementary to the ion survivor model of Karas et al., assumes that two energy-dependent processes exist: (i) a soft desolvation involving consecutive losses of neutral matrix molecules, leading to a multiply-charged analyte and (ii) hard desolvation leading to a low charge state analyte, by consecutive losses of charged matrix molecules. These desolvations pathways are discussed in terms of kinetically limited processes. The efficiency of the two competitive desolvation processes seems related to the internal energy carried away by clusters during ablation.
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Affiliation(s)
- Sandra Alves
- Laboratoire de Chimie Structurale Organique et Biologique, UMR 7613, Université Pierre et Marie Curie, Bat F, BP 45, 4 place Jussieu, 75005 Paris, France
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29
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Stano M, Flosadottir HD, Ingolfsson O. Effective quenching of fragment formation in negative ion oligonucleotide matrix-assisted laser desorption/ionization mass spectrometry through sodium adduct formation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:3498-502. [PMID: 17072905 DOI: 10.1002/rcm.2768] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Metastable decay of the sodium-free and the sodium adducts of the negatively charged hexameric nucleotides 5'-d(TTXYTT)-3' (X and Y are dC, dG or dA) in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) is reported. We show that the sodium adduct formation may be used to quantitatively quench dissociation channels in oligonucleotide MALDI-MS, and we argue, that by means of effective steps in the sample preparation that lead to per-sodiation of the sample, the sample preparation and the mass resolution of oligonucleotide mass spectra in MALDI may be improved substantially. The dependency of the fragment formation on the degree of sodiation is also discussed in context with the underlying fragmentation mechanisms.
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Affiliation(s)
- Michal Stano
- University of Iceland Science Institute, Reykjavik, Iceland
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30
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Abstract
Matrix Assisted Laser Desorption/Ionization (MALDI) is a very widely used analytical method, but has been developed in a highly empirical manner. Deeper understanding of ionization mechanisms could help to design better methods and improve interpretation of mass spectra. This review summarizes current mechanistic thinking, with emphasis on the most common MALDI variant using ultraviolet laser excitation. A two-step framework is gaining acceptance as a useful model for many MALDI experiments. The steps are primary ionization during or shortly after the laser pulse, followed by secondary reactions in the expanding plume of desorbed material. Primary ionization in UV-MALDI remains somewhat controversial, the two main approaches are the cluster and pooling/photoionization models. Secondary events are less contentious, ion-molecule reaction thermodynamics and kinetics are often invoked, but details differ. To the extent that local thermal equilibrium is approached in the plume, the mass spectra may be straightforwardly interpreted in terms of charge transfer thermodynamics.
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31
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DeKeyser SS, Li L. Matrix-assisted laser desorption/ionization Fourier transform mass spectrometry quantitation via in cell combination. Analyst 2005; 131:281-90. [PMID: 16440095 DOI: 10.1039/b510831d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a novel method for quantitation using a Fourier transform mass spectrometer (FTMS) equipped with a MALDI ion source. The unique instrumental configuration of FTMS and its ion trapping and storing capabilities enable ion packets originating from two physically distinct samples to be combined in the ion cyclotron resonance (ICR) cell prior to detection. These features are exploited to combine analyte ions from two differentially labeled samples spotted separately and then combined in the ICR cell to generate a single mass spectrum containing isotopically paired peaks for quantitative comparison of relative ion abundances. The utility of this new quantitation via in cell combination (QUICC) approach is explored using peptide standards, a bovine serum albumin tryptic digest, and a crude neuronal tissue extract. We show that spectra acquired using the QUICC scheme are comparable to those obtained from premixing the isotopically labeled samples in solution. In addition, we show direct tissue in situ isotopic formaldehyde labeling of a crustacean neuroendocrine organ, thus demonstrating the potential application of the QUICC methodology for direct tissue quantitative analysis.
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Affiliation(s)
- Stephanie S DeKeyser
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705-2222, USA
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32
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Ivleva VB, Sapp LM, O'Connor PB, Costello CE. Ganglioside analysis by thin-layer chromatography matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1552-1560. [PMID: 16054389 DOI: 10.1016/j.jasms.2005.05.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 05/12/2005] [Accepted: 05/12/2005] [Indexed: 05/03/2023]
Abstract
Metastable decomposition of ions generated in matrix-assisted laser desorption/ionization (MALDI) mass spectrometers complicates analysis of biological samples that have labile bonds. Recently, several academic laboratories and manufacturers of commercial instruments have designed instruments that introduce a cooling gas into the ion source during the MALDI event and have shown that the resulting vibrational cooling stabilizes these labile bonds. In this study, we compared stabilization and detection of desorbed gangliosides on a commercial orthogonal time-of-flight (oTOF) instrument with results we reported previously that had been obtained on a home-built Fourier transform mass spectrometer. Decoupling of the desorption/ionization from the detection steps resulted in an opportunity for desorbing thin-layer chromatography (TLC)-separated gangliosides directly from a TLC plate without compromising mass spectral accuracy and resolution of the ganglioside analysis, thus coupling TLC and oTOF mass spectrometry. The application of a declustering potential allowed control of the matrix cluster and matrix adduct formation, and, thus, enhanced the detection of the gangliosides.
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Affiliation(s)
- Vera B Ivleva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, 02215, Boston, Massachusetts, USA
| | - Lisa M Sapp
- Perkin-Elmer Life and Analytical Sciences, Boston, Massachusetts, USA
| | - Peter B O'Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Catherine E Costello
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA.
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33
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Liu Z, Schey KL. Optimization of a MALDI TOF-TOF mass spectrometer for intact protein analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:482-490. [PMID: 15792717 DOI: 10.1016/j.jasms.2004.12.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Revised: 12/15/2004] [Accepted: 12/20/2004] [Indexed: 05/24/2023]
Abstract
A MALDI TOF-TOF instrument was optimized and evaluated for intact protein analysis by tandem mass spectrometry. Ion source voltages and delay times were adjusted to affect an up to a 10-fold improvement in fragment ion yield compared to data obtained using default settings employed in peptide analysis. For large peptides (3-4.5 kDa), up to 90% of all possible b- and y-fragment ions were observed, which provides sufficient information for de novo sequencing and unambiguous protein identification. Product ion signals associated with preferential cleavages C-terminal to aspartic acid and glutamic acid residues and N-terminal to proline residues became dominant with increased protein molecular weight. Matrix effects were also evaluated and, among the eight matrices examined, alpha-cyano-4-hydroxycinnamic acid (CHCA) was found to produce the best intact protein tandem mass spectra for proteins up to 12 kDa. Optimized performance yielded detection limits of 50-125 fmol for proteins of 4 and 12 kDa, respectively. This improved performance has yielded an instrument with potential to be a useful tool in proteomic investigations via analysis of intact proteins.
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Affiliation(s)
- Zhaoyang Liu
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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34
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Kononikhin AS, Nikolaev EN, Frankevich V, Zenobi R. Multiply charged ions in matrix-assisted laser desorption/ionization generated from electrosprayed sample layers. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2005; 11:257-9. [PMID: 16107739 DOI: 10.1255/ejms.729] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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35
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Okuno S, Oka K, Arakawa R. Oxidation of Ferrocene Derivatives in Desorption/Ionization on Porous Silicon. ANAL SCI 2005; 21:1449-51. [PMID: 16379384 DOI: 10.2116/analsci.21.1449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In matrix-assisted laser desorption/ionization (MALDI), the true molecular structures of some analytes are not represented by the observed ions due to a redox reaction. In earlier reports, electron transfer from analyte to chemical matrix has been proposed for the oxidation of ferrocene derivatives in MALDI. To address such a redox phenomenon in laser desorption/ionization processes, two ferrocene derivatives, FcCH2CH2Fc and FcCH2NMe2 [Fc:(CsHs)Fe(CsH4)], were analyzed by a matrix-free method, desorption/ionization on porous silicon (DIOS). The oxidized species, Fc+CH2NMe2 and FcCH2CH2Fc+, were detected in the DIOS mass spectra. The results suggested that electron transfer from the analytes to the sample target occurs during the ionization process.
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Affiliation(s)
- Shoji Okuno
- Japan Science and Technology Agency, Innovation Plaza Osaka, Wada Project Laboratory, 3-1-10 Technostage, Izumi, Osaka 594-1144, Japan
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OKUNO S, SHIMOMAE Y, WADA Y, ARAKAWA R. Laser Desorption/Ionization Mass Spectrometry on Porous Silicon and Its Application to Synthetic Polymers. BUNSEKI KAGAKU 2005. [DOI: 10.2116/bunsekikagaku.54.439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Shoji OKUNO
- Japan Science and Technology Agency, Wada Proteomics Project
| | | | - Yoshinao WADA
- Osaka Medical Center and Research Institute for Material and Child Health
| | - Ryuichi ARAKAWA
- Japan Science and Technology Agency, Wada Proteomics Project
- Department of Applied Chemistry, Kansai University
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Dashtiev M, Frankevich V, Zenobi R. Signal enhancement in matrix-assisted laser desorption/ionization by doping with Cu(II) chloride. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:289-291. [PMID: 15609376 DOI: 10.1002/rcm.1768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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Köcher T, Engström A, Zubarev RA. Fragmentation of Peptides in MALDI In-Source Decay Mediated by Hydrogen Radicals. Anal Chem 2005; 77:172-7. [PMID: 15623293 DOI: 10.1021/ac0489115] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) shares some similarities with the novel fragmentation technique electron capture dissociation (ECD). In both reactions, the otherwise strong N-C(alpha) bond is cleaved, forming fragment ions of the c and z types, while labile posttranslational modifications are preserved. Therefore, it is tempting to assume that ISD and ECD have some mechanistic aspects in common. Because electrons are present in the MALDI plume, we investigated the previously suggested possibility that ISD is a variation of ECD. However, experiments with peptides with only one site for efficient protonation revealed that ISD is not caused by electron capture. Instead, ICD seems to be induced by hydrogen atoms generated by a photochemical reaction of the matrix. We provide evidence for this reaction by hydrogen/deuterium exchange experiments with peptides containing a minimal number of exchangeable hydrogen atoms. The hydrogen atom model in ECD is indirectly supported by the proposed fragmentation mechanism for ISD, because our data suggest that hydrogen radicals can induce fragmentation by cleavage of the N-C(alpha) bond, independent from their origin.
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Affiliation(s)
- Thomas Köcher
- Laboratory for Biological and Medical Mass Spectrometry, Uppsala University, Husargatan 3, Box 583, SE-75123 Uppsala, Sweden.
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Abstract
The recently developed model for primary and secondary UV-MALDI ion formation (Knochenmuss, R. J. Mass Spectrom. 2002, 37, 867-877. Knochenmuss, R. Anal. Chem. 2003, 75, 2199.) is applied to questions regarding photoionization pathways and electron versus negative ion production. Two-photon ionization of the matrix in direct contact with analyte is possible under some circumstances (Kinsel, G.; Knochenmuss, R.; Setz, P.; Land, C. M.; Goh, S.-K.; Archibong, E. F.; Hardesty, J. H.; Marynik, D. J. Mass Spectrom. 2002, 37, 1131-1140.), and is added to the model. When analyte is present in large mole ratios (such as when matrix suppression is desired), this effect contributes modestly to the ion yield. Generally, matrix exciton pooling remains dominant. The interfacial layer of thin samples on a metal substrate may also be ionizable in a 2-photon process. A mechanism is proposed, and the correspondingly modified model gives excellent agreement with electron emission versus laser intensity data. Capture in, or escape of low-energy electrons from a thick sample (or on a nonmetallic substrate) is also examined. Because the mean free path for MALDI electrons in a solid matrix is on the order of 10 nm, below such depths, any electrons generated are captured to form negative ions. Only a surface layer can emit free electrons. This surface emission effect is also well reproduced by the model, up to a laser intensity limit caused by surface charging. This charging phenomenon is investigated and illustrated by molecular dynamics calculations.
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Affiliation(s)
- Richard Knochenmuss
- Novartis Institutes for Biomedical Research, WSJ 503.11.04, 4002 Basel, Switzerland.
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Okuno S, Nakano M, Matsubayashi GE, Arakawa R, Wada Y. Reduction of organic dyes in matrix-assisted laser desorption/ionization and desorption/ionization on porous silicon. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2004; 18:2811-2817. [PMID: 15517555 DOI: 10.1002/rcm.1689] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Reduction of analytes in matrix-assisted laser desorption/ionization (MALDI) often obscures the actual determination of molecular structure. To address the redox reactions in laser desorption/ionization processes, the organic dyes Methylene Blue, Janus Green B, Crystal Violet and Rhodamine B were analyzed by MALDI or by desorption/ionization on porous silicon (DIOS). Susceptibility to reduction in MALDI was dependent on both the reduction potentials of analytes and the molar ratio of analyte to matrix molecules. Addition of Cu(II) ions as an electron scavenger suppressed the reduction of Methylene Blue in MALDI. The results suggested that electron transfer to analytes from the sample target and/or from the matrix contributed to the reduction. In DIOS, the reductions of organic dyes were more prominent than in MALDI, and were not prevented by Cu(II) ion doping, probably due to direct contact of the analytes with silicon which had little electric resistance.
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Affiliation(s)
- Shoji Okuno
- Japan Science and Technology Agency, Innovation Plaza Osaka, Wada Project Laboratory, 3-1-10 Technostage, Izumi, Osaka 594-1144, Japan.
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