1
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Parker K, Bollis NE, Ryzhov V. Ion-molecule reactions of mass-selected ions. MASS SPECTROMETRY REVIEWS 2024; 43:47-89. [PMID: 36447431 DOI: 10.1002/mas.21819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gas-phase reactions of mass-selected ions with neutrals covers a very broad area of fundamental and applied mass spectrometry (MS). Oftentimes, ion-molecule reactions (IMR) can serve as a viable alternative to collision-induced dissociation and other ion dissociation techniques when using tandem MS. This review focuses on the literature pertaining applications of IMR since 2013. During the past decade considerable efforts have been made in analytical applications of IMR, including advances in one of the major techniques for characterization of unsaturated fatty acids and lipids, ozone-induced dissociation, and the development of a new technique for sequencing of large ions, hydrogen atom attachment/abstraction dissociation. Many advances have also been made in identifying gas-phase chemistry specific to a functional group in organic and biological compounds, which are useful in structure elucidation of analytes and differentiation of isomers/isobars. With "soft" ionization techniques like electrospray ionization having become mainstream for quite some time now, the efforts in the area of metal ion catalysis have firmly moved into exploring chemistry of ligated metal complexes in their "natural" oxidation states allowing to model individual steps of mechanisms in homogeneous catalysis, especially in combination with high-level DFT calculations. Finally, IMR continue to contribute to the body of knowledge in the area of chemistry of interstellar processes.
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Affiliation(s)
- Kevin Parker
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
| | - Nicholas E Bollis
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
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2
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Lee ST, Park H, Jang I, Lee CS, Moon B, Oh HB. New free radical-initiated peptide sequencing (FRIPS) mass spectrometry reagent with high conjugation efficiency enabling single-step peptide sequencing. Sci Rep 2022; 12:9494. [PMID: 35680949 PMCID: PMC9184593 DOI: 10.1038/s41598-022-13624-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/17/2022] [Indexed: 12/04/2022] Open
Abstract
A newly designed TEMPO-FRIPS reagent, 4-(2,2,6,6-tetramethylpiperidine-1-oxyl) methyl benzyl succinic acid N-hydroxysuccinimide ester or p-TEMPO–Bn–Sc–NHS, was synthesized to achieve single-step free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) for a number of model peptides, including phosphopeptides. The p-TEMPO–Bn–Sc–NHS reagent was conjugated to target peptides, and the resulting peptides were subjected to collisional activation. The peptide backbone dissociation behaviors of the MS/MS and MS3 experiments were monitored in positive ion mode. Fragment ions were observed even at the single-step thermal activation of the p-TEMPO–Bn–Sc–peptides, showing mainly a-/x- and c-/z-type fragments and neutral loss ions. This confirms that radical-driven peptide backbone dissociations occurred with the p-TEMPO–Bn–Sc–peptides. Compared to the previous version of the TEMPO reagent, i.e., o-TEMPO–Bz–C(O)–NHS, the newly designed p-TEMPO–Bn–Sc–NHS has better conjugation efficiency for the target peptides owing to its improved structural flexibility and solubility in the experimental reagents. An energetic interpretation using the survival fraction as a function of applied normalized collision energy (NCE) ascertained the difference in the thermal activation between p-TEMPO–Bn–Sc– and o-TEMPO–Bz–C(O)– radical initiators. This study clearly demonstrates that the application of the p-TEMPO–Bn–Sc– radical initiator can improve the duty cycle, and this FRIPS MS approach has the potential to be implemented in proteomics studies, including phosphoproteomics.
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Affiliation(s)
- Sang Tak Lee
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Hyemi Park
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Inae Jang
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Choong Sik Lee
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.,Department of Toxicology and Chemistry, Scientific Investigation Laboratory, Criminal Investigation Command, Ministry of National Defense, Seoul, 04351, Korea
| | - Bongjin Moon
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
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3
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Lee JU, Lee ST, Park CR, Moon B, Kim HI, Oh HB. TEMPO-Assisted Free-Radical-Initiated Peptide Sequencing Mass Spectrometry for Ubiquitin Ions: An Insight on the Gas-Phase Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:471-481. [PMID: 35099967 DOI: 10.1021/jasms.1c00313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
TEMPO ((2,2,6,6-tetramethylpiperidine-1-yl)oxyl)-assisted free-radical-initiated peptide sequencing mass spectrometry (FRIPS MS) is applied to the top-down tandem mass spectrometry of guanidinated ubiquitin (UB(Gu)) ions, i.e., p-TEMPO-Bn-Sc-guanidinated ubiquitin (UBT(Gu)), to shed a light on gas-phase ubiquitin conformations. Thermal activation of UBT(Gu) ions produced protein backbone fragments of radical character, i.e., a-/x- and c-/z-type fragments. It is in contrast to the collision-induced dissociation (CID) results for UB(Gu), which dominantly showed the specific charge-remote CID fragments of b-/y-type at the C-terminal side of glutamic acid (E) and aspartic acid (D). The transfer of a radical "through space" was mainly observed for the +5 and +6 UBT(Gu) ions. This provides the information about folding/unfolding and structural proximity between the positions of the incipient benzyl radical site and fragmented sites. The analysis of FRIPS MS results for the +5 charge state ubiquitin ions shows that the +5 charge state ubiquitin ions bear a conformational resemblance to the native ubiquitin (X-ray crystallography structure), particularly in the central sequence region, whereas some deviations were observed in the unstable second structure region (β2) close to the N-terminus. The ion mobility spectrometry results also corroborate the FRIPS MS results in terms of their conformations (or structures). The experimental results obtained in this study clearly demonstrate a potential of the TEMPO-assisted FRIPS MS as one of the methods for the elucidation of the overall gas-phase protein structures.
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Affiliation(s)
- Jae-Ung Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Sang Tak Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Chae Ri Park
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Bongjin Moon
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
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4
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Wu R, Metternich JB, Tiwari P, Zenobi R. Adapting a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Gas-Phase Fluorescence Spectroscopy Measurement of Trapped Biomolecular Ions. Anal Chem 2021; 93:15626-15632. [PMID: 34784193 DOI: 10.1021/acs.analchem.1c02858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas-phase fluorescence spectroscopy is still in its infancy, which demands further instrumental developments. In this study, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), equipped with a lab-developed data acquisition system, was coupled to a tunable femtosecond laser and a state-of-the-art optical system for fluorescence studies of mass-selected ions. For excitation, a laser beam was focused (beam size < 1.0 mm) into the cylindrical ICR cell. A wire mesh replaced the back trapping plate, allowing ∼10% of the fluorescence emitted from trapped ions to be collected by a lens installed beside the wire mesh. The collected fluorescence light was then transmitted outside of the mass spectrometer via fiber optics. A novel accumulation during detection (ADD) scheme was developed to increase the duty cycle of gas-phase fluorescence spectroscopy experiments. With ADD, >90% duty cycle for mass spectrometry and fluorescence experiments could be achieved. This instrument was able to perform fluorescence experiments on various ions, from simple rhodamine dyes to large biomolecules (i.e., peptides and proteins) labeled with dyes of various optical properties. A fluorescence lifetime measurement of trapped rhodamine 6G cations was also performed, yielding a value of 5.97 ± 0.23 ns. This setup has a broad mass range and decent fluorescence spectroscopy performance (i.e., the emission spectrum of rhodamine 6G can be acquired with good S/N in a minute). Finally, this setup also allows more challenging gas-phase fluorescence spectroscopy experiments, for example, of low quantum yield fluorophores and large biomolecules in their native state that appear at high m/z, which may not be doable with quadrupole ion traps (QIT).
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Affiliation(s)
- Ri Wu
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Jonas B Metternich
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Prince Tiwari
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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5
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Lee JU, Kim Y, Kim WY, Oh HB. Graph theory-based reaction pathway searches and DFT calculations for the mechanism studies of free radical-initiated peptide sequencing mass spectrometry (FRIPS MS): a model gas-phase reaction of GGR tri-peptide. Phys Chem Chem Phys 2020; 22:5057-5069. [PMID: 32073000 DOI: 10.1039/c9cp05433b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Graph theory-based reaction pathway searches (ACE-Reaction program) and density functional theory calculations were performed to shed light on the mechanisms for the production of [an + H]+, xn+, yn+, zn+, and [yn + 2H]+ fragments formed in free radical-initiated peptide sequencing (FRIPS) mass spectrometry measurements of a small model system of glycine-glycine-arginine (GGR). In particular, the graph theory-based searches, which are rarely applied to gas-phase reaction studies, allowed us to investigate reaction mechanisms in an exhaustive manner without resorting to chemical intuition. As expected, radical-driven reaction pathways were favorable over charge-driven reaction pathways in terms of kinetics and thermodynamics. Charge- and radical-driven pathways for the formation of [yn + 2H]+ fragments were carefully compared, and it was revealed that the [yn + 2H]+ fragments observed in our FRIPS MS spectra originated from the radical-driven pathway, which is in contrast to the general expectation. The acquired understanding of the FRIPS fragmentation mechanism is expected to aid in the interpretation of FRIPS MS spectra. It should be emphasized that graph theory-based searches are powerful and effective methods for studying reaction mechanisms, including gas-phase reactions in mass spectrometry.
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Affiliation(s)
- Jae-Ung Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea.
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6
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Jang I, Jeon A, Lim SG, Hong DK, Kim MS, Jo JH, Lee ST, Moon B, Oh HB. Free Radical-Initiated Peptide Sequencing Mass Spectrometry for Phosphopeptide Post-translational Modification Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:538-547. [PMID: 30414067 DOI: 10.1007/s13361-018-2100-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
Free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) was employed to analyze a number of representative singly or doubly protonated phosphopeptides (phosphoserine and phosphotyrosine peptides) in positive ion mode. In contrast to collision-activated dissociation (CAD) results, a loss of a phosphate group occurred to a limited degree for both phosphoserine and phosphotyrosine peptides, and thus, localization of a phosphorylated site was readily achieved. Considering that FRIPS MS supplies a substantial amount of collisional energy to peptides, this result was quite unexpected because a labile phosphate group was conserved. Analysis of the resulting peptide fragments revealed the extensive production of a-, c-, x-, and z-type fragments (with some minor b- and y-type fragments), suggesting that radical-driven peptide fragmentation was the primary mechanism involved in the FRIPS MS of phosphopeptides. Results of this study clearly indicate that FRIPS MS is a promising tool for the characterization of post-translational modifications such as phosphorylation. Graphical Abstract.
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Affiliation(s)
- Inae Jang
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Aeran Jeon
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Suk Gyu Lim
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Seoul National University, Seoul, 08826, Republic of Korea
| | - Duk Ki Hong
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Soo Kim
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Korea University, Seoul, 02841, Republic of Korea
| | - Jae Hyeong Jo
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Sang Tak Lee
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Bongjin Moon
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea.
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7
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Iacobucci C, Schäfer M, Sinz A. Free radical-initiated peptide sequencing (FRIPS)-based cross-linkers for improved peptide and protein structure analysis. MASS SPECTROMETRY REVIEWS 2019; 38:187-201. [PMID: 29660147 DOI: 10.1002/mas.21568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Free radical-initiated peptide sequencing (FRIPS) has recently been introduced as an analytical strategy to create peptide radical ions in a predictable and effective way by collisional activation of specifically modified peptides ions. FRIPS is based on the unimolecular dissociation of open-shell ions and yields fragments that resemble those obtained by electron capture dissociation (ECD) or electron transfer dissociation (ETD). In this review article, we describe the fundamentals of FRIPS and highlight its fruitful combination with chemical cross-linking/mass spectrometry (MS) as a highly promising option to derive complementary structural information of peptides and proteins. FRIPS does not only yield exhaustive sequence information of cross-linked peptides, but also defines the exact cross-linking sites of the connected peptides. The development of more advanced FRIPS cross-linkers that extend the FRIPS-based cross-linking/MS approach to the study of large protein assemblies and protein interaction networks can be eagerly anticipated.
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Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), D-06120, Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Cologne, D-50939, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), D-06120, Germany
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8
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Wong YLE, Chen X, Wu R, Hung YLW, Yeung HS, Chan TWD. Generation and Characterization of Gas-Phase Doubly Charged Biradical Peptide Ions (M2+••). Anal Chem 2017; 89:7773-7780. [DOI: 10.1021/acs.analchem.7b01808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Y. L. Elaine Wong
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Xiangfeng Chen
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Key
Laboratory for Applied Technology of Sophisticated Analytical Instruments,
Shandong Analysis and Test Centre, Shandong Academy of Sciences, Jinan, Shandong, People’s Republic of China
| | - Ri Wu
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Y. L. Winnie Hung
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hoi Sze Yeung
- Bruker Scientific
Instruments Hong Kong Co. Limited, Kowloon Bay, Hong Kong SAR
| | - T.-W. Dominic Chan
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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9
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Mu X, Lau JKC, Lai CK, Siu KWM, Hopkinson AC, Chu IK. Isomerization versus dissociation of phenylalanylglycyltryptophan radical cations. Phys Chem Chem Phys 2017. [PMID: 28631796 DOI: 10.1039/c7cp02355c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four isomers of the radical cation of tripeptide phenylalanylglycyltryptophan, in which the initial location of the radical center is well defined, have been isolated and their collision-induced dissociation (CID) spectra examined. These ions, the π-centered [FGWπ˙]+, α-carbon- [FGα˙W]+, N-centered [FGWN˙]+ and ζ-carbon- [Fζ˙GW]+ radical cations, were generated via collision-induced dissociation (CID) of transition metal-ligand-peptide complexes, side chain fragmentation of a π-centered radical cation, homolytic cleavage of a labile nitrogen-nitrogen single bond, and laser induced dissociation of an iodinated peptide, respectively. The π-centered and tryptophan N-centered peptide radical cations produced almost identical CID spectra, despite the different locations of their initial radical sites, which indicated that interconversion between the π-centered and tryptophan N-centered radical cations is facile. By contrast, the α-carbon-glycyl radical [FGα˙W]+, and ζ-phenyl radical [Fζ˙GW]+, featured different dissociation product ions, suggesting that the interconversions among α-carbon, π-centered (or tryptophan N-centered) and ζ-carbon-radical cations have higher barriers than those to dissociation. Density functional theory calculations have been used to perform systematic mechanistic investigations on the interconversions between these isomers and to study selected fragmentation pathways for these isomeric peptide radical cations. The results showed that the energy barrier for interconversion between [FGWπ˙]+ and [FGWN˙]+ is only 31.1 kcal mol-1, much lower than the barriers to their dissociation (40.3 kcal mol-1). For the [FGWπ˙]+, [FGα˙W]+, and [Fζ˙GW]+, the barriers to interconversion are higher than those to dissociation, suggesting that interconversions among these isomers are not competitive with dissociations. The [z3 - H]˙+ ions isolated from [FGα˙W]+ and [Fζ˙GW]+ show distinctly different fragmentation patterns, indicating that the structures of these ions are different and this result is supported by the DFT calculations.
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Affiliation(s)
- Xiaoyan Mu
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
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10
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Mu X, Song T, Siu CK, Chu IK. Tautomerization and Dissociation of Molecular Peptide Radical Cations. CHEM REC 2017. [DOI: 10.1002/tcr.201700013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiaoyan Mu
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
| | - Tao Song
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
| | - Chi-Kit Siu
- Department of Biology and Chemistry; City University of Hong Kong; 83 Tat Chee Avenue Kowloon Tong, Hong Kong SAR P. R. China
| | - Ivan K. Chu
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
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11
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Jang I, Lee SY, Hwangbo S, Kang D, Lee H, Kim HI, Moon B, Oh HB. TEMPO-Assisted Free Radical-Initiated Peptide Sequencing Mass Spectrometry (FRIPS MS) in Q-TOF and Orbitrap Mass Spectrometers: Single-Step Peptide Backbone Dissociations in Positive Ion Mode. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:154-163. [PMID: 27686973 DOI: 10.1007/s13361-016-1508-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/15/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
The present study demonstrates that one-step peptide backbone fragmentations can be achieved using the TEMPO [2-(2,2,6,6-tetramethyl piperidine-1-oxyl)]-assisted free radical-initiated peptide sequencing (FRIPS) mass spectrometry in a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer and a Q-Exactive Orbitrap instrument in positive ion mode, in contrast to two-step peptide fragmentation in an ion-trap mass spectrometer (reference Anal. Chem. 85, 7044-7051 (30)). In the hybrid Q-TOF and Q-Exactive instruments, higher collisional energies can be applied to the target peptides, compared with the low collisional energies applied by the ion-trap instrument. The higher energy deposition and the additional multiple collisions in the collision cell in both instruments appear to result in one-step peptide backbone dissociations in positive ion mode. This new finding clearly demonstrates that the TEMPO-assisted FRIPS approach is a very useful tool in peptide mass spectrometry research. Graphical Abstract ᅟ.
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Affiliation(s)
- Inae Jang
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Sun Young Lee
- College of Pharmacy, Kyung Hee University, Seoul, 02447, Korea
| | - Song Hwangbo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Dukjin Kang
- Center for Bioanalysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea
| | - Hookeun Lee
- Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul, 02841, Korea
| | - Bongjin Moon
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
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12
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Hage C, Ihling CH, Götze M, Schäfer M, Sinz A. Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:56-68. [PMID: 27418170 DOI: 10.1007/s13361-016-1426-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/14/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS3 experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids. Graphical Abstract ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany
| | - Christian H Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany
| | - Michael Götze
- Institute of Biochemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle, Saale, Germany
| | - Mathias Schäfer
- Department of Chemistry, University Cologne, Greinstr. 4, D-50939, Köln, Germany.
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany.
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13
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Hendricks NG, Julian RR. Leveraging ultraviolet photodissociation and spectroscopy to investigate peptide and protein three-dimensional structure with mass spectrometry. Analyst 2016; 141:4534-40. [DOI: 10.1039/c6an01020b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in mass spectrometry and lasers have facilitated the development of novel experiments combining the benefits of both technologies.
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Affiliation(s)
| | - Ryan R. Julian
- Department of Chemistry
- University of California
- Riverside
- USA
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14
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Zhang J, Gao W, Fang RH, Dong A, Zhang L. Synthesis of Nanogels via Cell Membrane-Templated Polymerization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4309-13. [PMID: 26044721 PMCID: PMC4562875 DOI: 10.1002/smll.201500987] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/13/2015] [Indexed: 05/19/2023]
Abstract
The synthesis of biomimetic hydrogel nanoparticles coated with a natural cell membrane is described. Compared to the existing strategy of wrapping cell membranes onto pre-formed nanoparticle substrates, this new approach forms the cell membrane-derived vesicles first, followed by growing nanoparticle cores in situ. It adds significant controllability over the nanoparticle properties and opens unique opportunities for a broad range of biomedical applications.
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Affiliation(s)
- Jianhua Zhang
- Department of Nanoengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA. Department of Polymer Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Weiwei Gao
- Department of Nanoengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ronnie H. Fang
- Department of Nanoengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anjie Dong
- Department of Polymer Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Liangfang Zhang
- Department of Nanoengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
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Ihling C, Falvo F, Kratochvil I, Sinz A, Schäfer M. Dissociation behavior of a bifunctional tempo-active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:396-406. [PMID: 25800022 DOI: 10.1002/jms.3543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/28/2014] [Accepted: 11/12/2014] [Indexed: 06/04/2023]
Abstract
We have synthesized a homobifunctional active ester cross-linking reagent containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) moiety connected to a benzyl group (Bz), termed TEMPO-Bz-linker. The aim for designing this novel cross-linker was to facilitate MS analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). The TEMPO-Bz-linker was reacted with all 20 proteinogenic amino acids as well as with model peptides to gain detailed insights into its fragmentation mechanism upon collision activation. The final goal of this proof-of-principle study was to evaluate the potential of the TEMPO-Bz-linker for chemical cross-linking studies to derive 3D-structure information of proteins. Our studies were motivated by the well documented instability of the central NO-C bond of TEMPO-Bz reagents upon collision activation. The fragmentation of this specific bond was investigated in respect to charge states and amino acid composition of a large set of precursor ions resulting in the identification of two distinct fragmentation pathways. Molecular ions with highly basic residues are able to keep the charge carriers located, i.e. protons or sodium cations, and consequently decompose via a homolytic cleavage of the NO-C bond of the TEMPO-Bz-linker. This leads to the formation of complementary open-shell peptide radical cations, while precursor ions that are protonated at the TEMPO-Bz-linker itself exhibit a charge-driven formation of even-electron product ions upon collision activation. MS(3) product ion experiments provided amino acid sequence information and allowed determining the cross-linking site. Our study fully characterizes the CID behavior of the TEMPO-Bz-linker and demonstrates its potential, but also its limitations for chemical cross-linking applications utilizing the special features of open-shell peptide ions on the basis of selective tandem MS analysis.
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Affiliation(s)
- Christian Ihling
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
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Nam J, Kwon H, Jang I, Jeon A, Moon J, Lee SY, Kang D, Han SY, Moon B, Oh HB. Bromine isotopic signature facilitates de novo sequencing of peptides in free-radical-initiated peptide sequencing (FRIPS) mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:378-387. [PMID: 25800020 DOI: 10.1002/jms.3539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 08/04/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
We recently showed that free-radical-initiated peptide sequencing mass spectrometry (FRIPS MS) assisted by the remarkable thermochemical stability of (2,2,6,6-tetramethyl-piperidin-1-yl)oxyl (TEMPO) is another attractive radical-driven peptide fragmentation MS tool. Facile homolytic cleavage of the bond between the benzylic carbon and the oxygen of the TEMPO moiety in o-TEMPO-Bz-C(O)-peptide and the high reactivity of the benzylic radical species generated in •Bz-C(O)-peptide are key elements leading to extensive radical-driven peptide backbone fragmentation. In the present study, we demonstrate that the incorporation of bromine into the benzene ring, i.e. o-TEMPO-Bz(Br)-C(O)-peptide, allows unambiguous distinction of the N-terminal peptide fragments from the C-terminal fragments through the unique bromine doublet isotopic signature. Furthermore, bromine substitution does not alter the overall radical-driven peptide backbone dissociation pathways of o-TEMPO-Bz-C(O)-peptide. From a practical perspective, the presence of the bromine isotopic signature in the N-terminal peptide fragments in TEMPO-assisted FRIPS MS represents a useful and cost-effective opportunity for de novo peptide sequencing.
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Affiliation(s)
- Jungjoo Nam
- Department of Chemistry, Sogang University, Seoul, 121-742, Korea
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Lai CK, Mu X, Hao Q, Hopkinson AC, Chu IK. Formation, isomerization, and dissociation of ε- and α-carbon-centered tyrosylglycylglycine radical cations. Phys Chem Chem Phys 2014; 16:24235-43. [DOI: 10.1039/c4cp03119a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CID spectra of [Yε˙GG]+ and [YGGα˙]+ are identical, showing that interconversion occurs prior to dissociation. For [Yε˙GG]+, [Yπ˙GG]+ and [YGα˙G]+, the dissociation products are all distinctly different, indicating that dissociation occurs more readily than isomerization.
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Affiliation(s)
- Cheuk-Kuen Lai
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, China
| | - Xiaoyan Mu
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, China
| | - Qiang Hao
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, China
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto, Canada
| | - Ivan K. Chu
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, China
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