1
|
Wu Y, Liu P, Liao Q, Jin T, Wu Z, Guomin W, Wang H, Chu PK. Cotton Fibers with a Lactic Acid-Like Surface for Re-establishment of Protective Lactobacillus Microbiota by Selectively Inhibiting Vaginal Pathogens. Adv Healthc Mater 2024; 13:e2302736. [PMID: 38061349 DOI: 10.1002/adhm.202302736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Failure to reconstruct the Lactobacillus microbiota is the major reason for the recurrence of vaginal infection. However, most empiric therapies focus on the efficacy of pathogen elimination but do not sufficiently consider the viability of Lactobacillus. Herein, cotton fibers with a lactic acid-like surface (LC) are fabricated by NaIO4 oxidation and L-isoserine grafting. The lactic acid analog chain ends and imine structure of LC can penetrate cell walls to cause protein cleavage in Escherichia coli and Candida albicans and inhibit vaginal pathogens. Meanwhile, the viability of Lactobacillus acidophilus is unaffected by the LC treatment, thus revealing a selective way to suppress pathogens as well as provide a positive route to re-establish protective microbiota in the vaginal tract. Moreover, LC has excellent properties such as good biosafety, antiadhesion, water absorption, and weight retention. The strategy proposed here not only is practical, but also provides insights into the treatment of vaginal infections.
Collapse
Affiliation(s)
- Yuzheng Wu
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Pei Liu
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Qing Liao
- Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- School of Nuclear Science and Technology and CAS Key Laboratory of Geospace Environment, University of Science and Technology of China, Hefei, 230026, China
| | - Tao Jin
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- School of Nuclear Science and Technology and CAS Key Laboratory of Geospace Environment, University of Science and Technology of China, Hefei, 230026, China
| | - Zhengwei Wu
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Wang Guomin
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Huaiyu Wang
- Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Paul K Chu
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| |
Collapse
|
2
|
Osho KE, Wasik KA, Geary LM, Borotto NB. Improved Performance of Positive-Ion Mode Free Radical-Initiated Peptide Sequencing with p-TEMPO-Bz. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:579-585. [PMID: 36820620 PMCID: PMC10515654 DOI: 10.1021/jasms.2c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Free radical-initiated peptide sequencing (FRIPS) is a tandem mass spectrometry technique that generates sequence informative ions via collisionally initiated radical chemistry. Collision activation homolytically cleaves an installed radical precursor and initiates radical formation, extensive hydrogen atom transfer, and peptide backbone dissociation. While the FRIPS technique shows great promise, when applied to multiply charged derivatized peptide ions, a series of high-abundance mass losses are observed which siphon ion abundance from radically generated sequence ions. This loss of ion abundance reduces the sequence coverage generated by FRIPS fragmentation. In this work, we hypothesized that these mass losses were assisted by the ortho-orientation of the radical precursor undergoing facile conversion into five- or six-membered intermediates or products and that when combined with the lower bond dissociation energy of the para-precursor, conjugated peptides would not undergo this chemistry. To test this assertion, we synthesized p-TEMPO-Bz, conjugated it to these peptides, and collisionally activated each. Indeed, we see dramatic attenuation of these undesired collisional processes and a significant increase in radical precursor ion abundance. The increase in ion abundance leads to a significant increase in the sequence coverage generated. These results demonstrate that p-TEMPO-Bz significantly improves the performance of positive-ion mode FRIPS and may be a compelling alternative to the currently utilized o-TEMPO-Bz-based FRIPS.
Collapse
Affiliation(s)
- Kemi E. Osho
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Kimberly A. Wasik
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Laina M. Geary
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Nicholas B. Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| |
Collapse
|
3
|
Ramírez CR, Murtada R, Gao J, Ruotolo BT. Free Radical-Based Sequencing for Native Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2283-2290. [PMID: 36346751 PMCID: PMC10202123 DOI: 10.1021/jasms.2c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Native top-down proteomics allows for both proteoform identification and high-order structure characterization for cellular protein complexes. Unfortunately, tandem MS-based fragmentation efficiencies for such targets are low due to an increase in analyte ion mass and the low ion charge states that characterize native MS data. Multiple fragmentation methods can be integrated in order to increase protein complex sequence coverage, but this typically requires use of specialized hardware and software. Free-radical-initiated peptide sequencing (FRIPS) enables access to charge-remote and electron-based fragmentation channels within the context of conventional CID experiments. Here, we optimize FRIPS labeling for native top-down sequencing experiments. Our labeling approach is able to access intact complexes with TEMPO-based FRIPS reagents without significant protein denaturation or assembly disruption. By combining CID and FRIPS datasets, we observed sequence coverage improvements as large as 50% for protein complexes ranging from 36 to 106 kDa. Fragment ion production in these experiments was increased by as much as 102%. In general, our results indicate that TEMPO-based FRIPS reagents have the potential to dramatically increase sequence coverage obtained in native top-down experiments.
Collapse
Affiliation(s)
- Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rayan Murtada
- Department of Chemistry & Biochemistry, Montclair State University, Montclair NJ 07043, United States
| | - Jinshan Gao
- Department of Chemistry & Biochemistry, Montclair State University, Montclair NJ 07043, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
4
|
Qian B, Zhang L, Zhang G, Fu Y, Zhu X, Shen G. Thermodynamic Evaluation on Alkoxyamines of TEMPO Derivatives, Stable Alkoxyamines or Potential Radical Donors? ChemistrySelect 2022. [DOI: 10.1002/slct.202204144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Bao‐Chen Qian
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| | - Lu Zhang
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| | - Gao‐Shuai Zhang
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| | - Yan‐Hua Fu
- College of Chemistry and Environmental Engineering Anyang Institute of Technology Anyang Henan 455000 P. R. China
| | - Xiao‐Qing Zhu
- The State Key Laboratory of Elemento-Organic Chemistry Department of Chemistry Nankai University Tianjin 300071 P. R. China
| | - Guang‐Bin Shen
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Yang X, Xia Y. Mapping Complex Disulfide Bonds via Implementing Photochemical Reduction Online with Liquid Chromatography-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:307-314. [PMID: 33136395 DOI: 10.1021/jasms.0c00324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Assigning disulfide linkage is a crucial task for protein identification. The current bottom-up proteomics workflow has limitations in characterizing peptide digests containing multiple disulfide bonds due to the difficulty of controlling partial reduction via conventional chemical reduction methods. Previously, our lab reported the development of an acetone/2-propanol (IPA) photoinitiating system for rapid (on second time scale) and tunable disulfide bond reduction. Herein, we incorporated this reaction system onto a liquid chromatography-mass spectrometry (LC-MS) system for bottom-up protein analysis applications. The photochemical reduction reaction was implemented in a flow microreactor which allowed for up to 15 s 254 nm UV irradiation. The microreactor was installed post LC separation and right before electrospray ionization, while a T-junction was used to introduce the photoinitiating solution to the LC eluent before entering the microreactor. The degree of disulfide reduction was tunable from partial reduction to complete reduction for peptides containing one or multiple disulfide bonds. Significantly improved sequence coverage was obtained from complete disulfide reduction, while assignment of the disulfide connectivity was facilitated from partial disulfide reduction when coupled with tandem mass spectrometry via collision-induced dissociation. As a proof-of-concept test, trypsin digests of lysozyme (four disulfide bonds) and bovine serum albumin (BSA, 17 disulfide bonds) were analyzed by the LC-MS system coupled with online reduction. Sequence coverage was improved from 35% to 100% and 13% to 87% for lysozyme and BSA, respectively. All four disulfide bonds of lysozyme were determined. For BSA, nine disulfide bonds were characterized and eight adjacent disulfide bonds were narrowed down.
Collapse
Affiliation(s)
- Xiaoyue Yang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
8
|
Kuo CM, Wei SY, Du SH, Lin JL, Chu CH, Chen CH, Tai JH, Chen SH. Comprehensive Workflow for Mapping Disulfide Linkages Including Free Thiols and Error Checking by On-Line UV-Induced Precolumn Reduction and Spiked Control. Anal Chem 2020; 93:1544-1552. [PMID: 33378175 DOI: 10.1021/acs.analchem.0c03866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mapping highly complicated disulfide linkages and free thiols via liquid chromatography-tandem mass spectrometry (LC-MS2) is challenging because of the difficulties in optimizing sample preparation to acquire critical MS data and detecting mispairings. Herein, we report a highly efficient and comprehensive workflow using an on-line UV-induced precolumn reduction tandem mass spectrometry (UV-LC-MS2) coupled with two-stage data analysis and spiked control. UV-LC-MS2 features a gradient run of acetonitrile containing a tunable percentage of photoinitiators (acetone/alcohol) that drives the sample to the MS through a UV-flow cell and reverse phase column to separate UV-induced products for subsequent fragmentation via low energy collision-induced dissociation. This allowed the alkylated thiol-containing and UV-reduced cysteine-containing peptides to be identified by a nontargeted database search. Expected or unexpected disulfide/thiol mapping was then carried out based on the search results, and data were derived from partially reduced species by photochemical reaction. Complete assignments of native and scrambled disulfide linkages of insulin, α-lactalbumin, and bovine serum albumin (BSA) as well as the free C34-BSA were demonstrated using none or single enzyme digestion. This workflow was applied to characterize unknown disulfide/thiol patterns of the recombinant cyclophilin 1 monomer (rTvCyP1 mono) from the human pathogen Trichomonas vaginalis. α-Lactalbumin was judiciously chosen as a spiked control to minimize mispairings due to sample preparation. rTvCyP1 was determined to contain a high percentage of thiol (>80%). The rest of rTvCyP1 mono were identified to contain two disulfide/thiol patterns, of which C41-C169 linkage was confirmed to exist as C53-C181 in rTvCyP2, a homologue of rTvCyP1. This platform identifies heterogeneous protein disulfide/thiol patterns in a de-novo fashion with artifact control, opening up an opportunity to characterize crude proteins for many applications.
Collapse
Affiliation(s)
- Chin-Ming Kuo
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Shih-Yao Wei
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Shu-Han Du
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Jung-Lee Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chien-Hsin Chu
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Jung-Hsiang Tai
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| |
Collapse
|
9
|
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.
Collapse
Affiliation(s)
- Jae-Ung Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea.
| | | | | | | |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Adhikari S, Yang X, Xia Y. Acetone/Isopropanol Photoinitiating System Enables Tunable Disulfide Reduction and Disulfide Mapping via Tandem Mass Spectrometry. Anal Chem 2018; 90:13036-13043. [PMID: 30350608 PMCID: PMC6310128 DOI: 10.1021/acs.analchem.8b04019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Herein, we report the development of a new photochemical system which enables rapid and tunable disulfide bond reduction and its application in disulfide mapping via online coupling with mass spectrometry (MS). Acetone, a clean and electrospray ionization (ESI) compatible solvent, is used as the photoinitiator (1% volume) in the solvent system consisting of 1:1 alkyl alcohol and water. Under ultraviolet (UV) irradiation (∼254 nm), the acetone/alcohol system produces hydroxyalkyl radicals, which are responsible for disulfide bond cleavage in peptides. Acetone/isopropanol is most suitable for optimizing the disulfide reduction products, leading to almost complete conversion in less than 5 s when the reaction is conducted in a flow microreactor. The flow microreactor device not only facilitates direct coupling with ESI-MS but also allows fine-tuning of the extent of disulfide reduction by varying the UV exposure time. Near full sequence coverage for peptides consisting of intra- or interchain disulfide bonds has been achieved from complete disulfide reduction and online tandem mass spectrometry (MS/MS) via low energy collision-induced dissociation. Coupling different degrees of partial disulfide reduction with ESI-MS/MS allows disulfide mapping as demonstrated for characterizing the three disulfide bonds in insulin.
Collapse
Affiliation(s)
- Sarju Adhikari
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Xiaoyue Yang
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yu Xia
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| |
Collapse
|
13
|
Rush MJ, Riley NM, Westphall MS, Coon JJ. Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation. Anal Chem 2018; 90:8946-8953. [PMID: 29949341 PMCID: PMC6434944 DOI: 10.1021/acs.analchem.8b01113] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here we report the fragmentation of disulfide linked intact proteins using activated-ion electron transfer dissociation (AI-ETD) for top-down protein characterization. This fragmentation method is then compared to the alternative methods of beam-type collisional activation (HCD), electron transfer dissociation (ETD), and electron transfer and higher-energy collision dissociation (EThcD). We analyzed multiple precursor charge states of the protein standards bovine insulin, α-lactalbumin, lysozyme, β-lactoglobulin, and trypsin inhibitor. In all cases, we found that AI-ETD provides a boost in protein sequence coverage information and the generation of fragment ions from within regions enclosed by disulfide bonds. AI-ETD shows the largest improvement over the other techniques when analyzing highly disulfide linked and low charge density precursor ions. This substantial improvement is attributed to the concurrent irradiation of the gas phase ions while the electron-transfer reaction is taking place, mitigating nondissociative electron transfer, helping unfold the gas phase protein during the electron transfer event, and preventing disulfide bond reformation. We also show that AI-ETD is able to yield comparable sequence coverage information when disulfide bonds are left intact relative to proteins that have been reduced and alkylated. This work demonstrates that AI-ETD is an effective fragmentation method for the analysis of proteins with intact disulfide bonds, dramatically enhancing sequence ion generation and total sequence coverage compared to HCD and ETD.
Collapse
Affiliation(s)
- Matthew J.P. Rush
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Nicholas M. Riley
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | | | - Joshua J. Coon
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| |
Collapse
|
14
|
Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.
Collapse
|
15
|
Durand KL, Tan L, Stinson CA, Love-Nkansah CB, Ma X, Xia Y. Assigning Peptide Disulfide Linkage Pattern Among Regio-Isomers via Methoxy Addition to Disulfide and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1099-1108. [PMID: 28194735 DOI: 10.1007/s13361-017-1595-1] [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: 11/07/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
Pinpointing disulfide linkage pattern is critical in the characterization of proteins and peptides consisting of multiple disulfide bonds. Herein, we report a method based on coupling online disulfide modification and tandem mass spectrometry (MS/MS) to distinguish peptide disulfide regio-isomers. Such a method relies on a new disulfide bond cleavage reaction in solution, involving methanol as a reactant and 254 nm ultraviolet (UV) irradiation. This reaction leads to selective cleavage of a disulfide bond and formation of sulfenic methyl ester (-SOCH3) at one cysteine residue and a thiol (-SH) at the other. Under low energy collision-induced dissociation (CID), cysteine sulfenic methyl ester motif produces a signature methanol loss (-32 Da), allowing its identification from other possible isomeric structures such as S-hydroxylmethyl (-SCH2OH) and methyl sulfoxide (-S(O)-CH3). Since disulfide bond can be selectively cleaved and modified upon methoxy addition, subsequent MS2 CID of the methoxy addition product provides enhanced sequence coverage as demonstrated by the analysis of bovine insulin. More importantly, this reaction does not induce disulfide scrambling, likely due to the fact that radical intermediates are not involved in the process. An approach based on methoxy addition followed by MS3 CID has been developed for assigning disulfide linkage patterns in peptide disulfide regio-isomers. This methodology was successfully applied to characterizing peptide systems having two disulfide bonds and three disulfide linkage isomers: side-by-side, overlapped, and looped-within-a-loop configurations. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Kirt L Durand
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Lei Tan
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Craig A Stinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | | | - Xiaoxiao Ma
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Yu Xia
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Wongkongkathep P, Li H, Zhang X, Loo RRO, Julian RR, Loo JA. Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:137-145. [PMID: 26644781 PMCID: PMC4669582 DOI: 10.1016/j.ijms.2015.07.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in combination with ECD allowed the three disulfide bonds of insulin to be cleaved and the overall sequence coverage to be increased. For the larger sized ribonuclease A with four disulfide bonds, irradiation from an infrared laser (10.6 µm) to disrupt non-covalent interactions was combined with UV-activation to facilitate the cleavage of up to three disulfide bonds. Preferences for disulfide bond cleavage are dependent on protein structure and sequence. Disulfide bonds can reform if the generated radicals remain in close proximity. By varying the time delay between the UV-activation and the ECD events, it was determined that disulfide bonds reform within 10-100 msec after their UV-homolytic cleavage.
Collapse
Affiliation(s)
- Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Huilin Li
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Xing Zhang
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521
| | - Rachel R. Ogorzalek Loo
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Ryan R. Julian
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles Los Angeles, CA 90095
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
- UCLA/DOE Institute of Genomics and Proteomics, University of California-Los Angeles Los Angeles, CA 90095
- Corresponding author at: University of California-Los Angeles, Department of Chemistry and Biochemistry, 402 Boyer Hall, Molecular Biology Institute, Los Angeles, CA, United States, Tel.: +1 310 794 7023; fax: +1 310 206 4038, (J.A. Loo)
| |
Collapse
|
18
|
Sohn CH, Gao J, Thomas DA, Kim TY, Goddard WA, Beauchamp JL. Mechanisms and energetics of free radical initiated disulfide bond cleavage in model peptides and insulin by mass spectrometry. Chem Sci 2015; 6:4550-4560. [PMID: 29142703 PMCID: PMC5666513 DOI: 10.1039/c5sc01305d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/20/2015] [Indexed: 11/21/2022] Open
Abstract
Direct radical substitution at sulfur initiates disulfide bond cleavage by hydrogen-deficient radicals in peptides and proteins.
We investigate the mechanism of disulfide bond cleavage in gaseous peptide and protein ions initiated by a covalently-attached regiospecific acetyl radical using mass spectrometry (MS). Highly selective S–S bond cleavages with some minor C–S bond cleavages are observed by a single step of collisional activation. We show that even multiple disulfide bonds in intact bovine insulin are fragmented in the MS2 stage, releasing the A- and B-chains with a high yield, which has been challenging to achieve by other ion activation methods. Yet, regardless of the previous reaction mechanism studies, it has remained unclear why (1) disulfide bond cleavage is preferred to peptide backbone fragmentation, and why (2) the S–S bond that requires the higher activation energy conjectured in previously suggested mechanisms is more prone to be cleaved than the C–S bond by hydrogen-deficient radicals. To probe the mechanism of these processes, model peptides possessing deuterated β-carbon(s) at the disulfide bond are employed. It is suggested that the favored pathway of S–S bond cleavage is triggered by direct acetyl radical attack at sulfur with concomitant cleavage of the S–S bond (SH2). The activation energy for this process is substantially lower by ∼9–10 kcal mol–1 than those of peptide backbone cleavage processes determined by density functional quantum chemical calculations. Minor reaction pathways are initiated by hydrogen abstraction from the α-carbon or the β-carbon of a disulfide, followed by β-cleavages yielding C–S or S–S bond scissions. The current mechanistic findings should be generally applicable to other radical-driven disulfide bond cleavages with different radical species such as the benzyl and methyl pyridyl radicals.
Collapse
Affiliation(s)
- Chang Ho Sohn
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Jinshan Gao
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Daniel A Thomas
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Tae-Young Kim
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - William A Goddard
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA . .,Materials and Process Simulation Center , Beckman Institute , California Institute of Technology , Pasadena , CA 91125 , USA
| | - J L Beauchamp
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| |
Collapse
|
19
|
Oh HB, Moon B. Radical-driven peptide backbone dissociation tandem mass spectrometry. MASS SPECTROMETRY REVIEWS 2015; 34:116-132. [PMID: 24863492 DOI: 10.1002/mas.21426] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 05/06/2013] [Accepted: 11/20/2013] [Indexed: 06/03/2023]
Abstract
In recent years, a number of novel tandem mass spectrometry approaches utilizing radical-driven peptide gas-phase fragmentation chemistry have been developed. These approaches show a peptide fragmentation pattern quite different from that of collision-induced dissociation (CID). The peptide fragmentation features of these approaches share some in common with electron capture dissociation (ECD) or electron transfer dissociation (ETD) without the use of sophisticated equipment such as a Fourier-transform mass spectrometer. For example, Siu and coworkers showed that CID of transition metal (ligand)-peptide ternary complexes led to the formation of peptide radical ions through dissociative electron transfer (Chu et al., 2000. J Phys Chem B 104:3393-3397). The subsequent collisional activation of the generated radical ions resulted in a number of characteristic product ions, including a, c, x, z-type fragments and notable side-chain losses. Another example is the free radical initiated peptide sequencing (FRIPS) approach, in which Porter et al. and Beauchamp et al. independently introduced a free radical initiator to the primary amine group of the lysine side chain or N-terminus of peptides (Masterson et al., 2004. J Am Chem Soc 126:720-721; Hodyss et al., 2005 J Am Chem Soc 127: 12436-12437). Photodetachment of gaseous multiply charged peptide anions (Joly et al., 2008. J Am Chem Soc 130:13832-13833) and UV photodissociation of photolabile radical precursors including a C-I bond (Ly & Julian, 2008. J Am Chem Soc 130:351-358; Ly & Julian, 2009. J Am Soc Mass Spectrom 20:1148-1158) also provide another route to generate radical ions. In this review, we provide a brief summary of recent results obtained through the radical-driven peptide backbone dissociation tandem mass spectrometry approach.
Collapse
Affiliation(s)
- Han Bin Oh
- Department of Chemistry, Sogang University, Seoul, 121-742, Republic of Korea
| | | |
Collapse
|
20
|
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.
Collapse
Affiliation(s)
- Christian Ihling
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
| | | | | | | | | |
Collapse
|
21
|
Gilbert JD, Fisher CM, Bu J, Prentice BM, Redwine JG, McLuckey SA. Strategies for generating peptide radical cations via ion/ion reactions. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:418-26. [PMID: 25800024 PMCID: PMC4372815 DOI: 10.1002/jms.3548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 11/14/2014] [Accepted: 11/16/2014] [Indexed: 05/25/2023]
Abstract
Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon-iodine (C-I) bond are subjected to UVPD with 266-nm photons, which selectively cleaves the C-I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even-electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non-covalent complexes in the electrospray process.
Collapse
Affiliation(s)
| | | | | | | | | | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey 560 Oval Drive Department of Chemistry Purdue University West Lafayette, IN 47907-2084, USA Phone: (765) 494-5270 Fax: (765) 494-0239
| |
Collapse
|
22
|
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.
Collapse
Affiliation(s)
- Jungjoo Nam
- Department of Chemistry, Sogang University, Seoul, 121-742, Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Lesslie M, Osburn S, van Stipdonk MJ, Ryzhov V. Gas-phase tyrosine-to-cysteine radical migration in model systems. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:589-597. [PMID: 26307738 DOI: 10.1255/ejms.1341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Radical migration, both intramolecular and intermolecular, from the tyrosine phenoxyl radical Tyr(O(∙)) to the cysteine radical Cys(S(∙)) in model peptide systems was observed in the gas phase. Ion-molecule reactions (IMRs) between the radical cation of homotyrosine and propyl thiol resulted in a fast hydrogen atom transfer. In addition, radical cations of the peptide LysTyrCys were formed via two different methods, affording regiospecific production of Tyr(O(∙)) or Cys(S(∙)) radicals. Collision-induced dissociation of these isomeric species displayed evidence of radical migration from the oxygen to sulfur, but not for the reverse process. This was supported by theoretical calculations, which showed the Cys(S(∙)) radical slightly lower in energy than the Tyr(O(∙)) isomer. IMRs of the LysTyrCys radical cation with allyl iodide further confirmed these findings. A mechanism for radical migration involving a proton shuttle by the C-terminal carboxylic group is proposed.
Collapse
Affiliation(s)
- Michael Lesslie
- Department of Chemistry and Biochemistry, and Center for Biochemical and Biophysical Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA.
| | - Sandra Osburn
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania15282, USA.
| | - Michael J van Stipdonk
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA.
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry, and Center for Biochemical and Biophysical Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA.
| |
Collapse
|
24
|
Thomas DA, Sohn CH, Gao J, Beauchamp JL. Hydrogen Bonding Constrains Free Radical Reaction Dynamics at Serine and Threonine Residues in Peptides. J Phys Chem A 2014; 118:8380-92. [DOI: 10.1021/jp501367w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Daniel A. Thomas
- Arthur Amos Noyes Laboratory
of Chemical Physics, California Institute of Technology, Pasadena, California 91125, United States
| | - Chang Ho Sohn
- Arthur Amos Noyes Laboratory
of Chemical Physics, California Institute of Technology, Pasadena, California 91125, United States
| | - Jinshan Gao
- Arthur Amos Noyes Laboratory
of Chemical Physics, California Institute of Technology, Pasadena, California 91125, United States
| | - J. L. Beauchamp
- Arthur Amos Noyes Laboratory
of Chemical Physics, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
25
|
Kwon G, Kwon H, Lee J, Han SY, Moon B, Oh HB, Sung BJ. Density Functional Theory (DFT) Study of Gas-phase O.C Bond Dissociation Energy of Models for o-TEMPO-Bz-C(O)-Peptide: A Model Study for Free Radical Initiated Peptide Sequencing. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.3.770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
26
|
Jia L, Chen K, Wang C, Yao J, Chen Z, Li H. Unexpected oxidation of β-isophorone with molecular oxygen promoted by TEMPO. RSC Adv 2014. [DOI: 10.1039/c3ra47901c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
27
|
Marshall DL, Hansen CS, Trevitt AJ, Oh HB, Blanksby SJ. Photodissociation of TEMPO-modified peptides: new approaches to radical-directed dissociation of biomolecules. Phys Chem Chem Phys 2014; 16:4871-9. [DOI: 10.1039/c3cp54825b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
28
|
Lee J, Park H, Kwon H, Kwon G, Jeon A, Kim HI, Sung BJ, Moon B, Oh HB. One-Step Peptide Backbone Dissociations in Negative-Ion Free Radical Initiated Peptide Sequencing Mass Spectrometry. Anal Chem 2013; 85:7044-51. [DOI: 10.1021/ac303517h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jihye Lee
- Department
of Chemistry, Sogang University, Seoul
121-742, Korea
| | - Hyeyeon Park
- Department
of Chemistry, Sogang University, Seoul
121-742, Korea
| | - Hyuksu Kwon
- Department
of Chemistry, Sogang University, Seoul
121-742, Korea
| | - Gyemin Kwon
- Department
of Chemistry, Sogang University, Seoul
121-742, Korea
| | - Aeran Jeon
- Department
of Chemistry, Sogang University, Seoul
121-742, Korea
| | - Hugh I. Kim
- Department
of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Bong June Sung
- Department
of Chemistry, Sogang University, Seoul
121-742, Korea
| | - Bongjin Moon
- Department
of Chemistry, Sogang University, Seoul
121-742, Korea
| | - Han Bin Oh
- Department
of Chemistry, Sogang University, Seoul
121-742, Korea
| |
Collapse
|
29
|
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
| | | |
Collapse
|
30
|
Tan L, Xia Y. Gas-phase reactivity of peptide thiyl (RS•), perthiyl (RSS•), and sulfinyl (RSO•) radical ions formed from atmospheric pressure ion/radical reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:534-542. [PMID: 23354473 DOI: 10.1007/s13361-012-0548-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/20/2012] [Accepted: 11/26/2012] [Indexed: 06/01/2023]
Abstract
In this study, we demonstrated the formation of gas-phase peptide perthiyl (RSS•) and thiyl (RS•) radical ions besides sulfinyl radical (RSO•) ions from atmospheric pressure (AP) ion/radical reactions of peptides containing inter-chain disulfide bonds. The identity of perthiyl radical was verified from characteristic 65 Da (•SSH) loss in collision-induced dissociation (CID). This signature loss was further used to assess the purity of peptide perthiyl radical ions formed from AP ion/radical reactions. Ion/molecule reactions combined with CID were carried out to confirm the formation of thiyl radical. Transmission mode ion/molecule reactions in collision cell (q2) were developed as a fast means to estimate the population of peptide thiyl radical ions. The reactivity of peptide thiyl, perthiyl, and sulfinyl radical ions was evaluated based on ion/molecule reactions toward organic disulfides, allyl iodide, organic thiol, and oxygen, which followed in order of thiyl (RS•) > perthiyl (RSS•) > sulfinyl (RSO•). The gas-phase reactivity of these three types of sulfur-based radicals is consistent with literature reports from solution studies.
Collapse
Affiliation(s)
- Lei Tan
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | |
Collapse
|
31
|
Clark DF, Go EP, Desaire H. Simple approach to assign disulfide connectivity using extracted ion chromatograms of electron transfer dissociation spectra. Anal Chem 2013; 85:1192-9. [PMID: 23210856 DOI: 10.1021/ac303124w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Increasing interest in production of protein-based pharmaceuticals (biotherapeutics) is accompanied by an increased need for verification of protein folding and correct disulfide bonding. Recombinant protein expression may produce aberrant disulfide bonds and could result in safety concerns or decreased efficacy. Thus, the thorough analysis of disulfide bonding is a necessity for protein therapeutics. The use of electron transfer dissociation (ETD) facilitates this analysis because disulfide bonds are preferentially cleaved when subjected to ETD. Here, we make use of this well-characterized reaction to assign disulfide bonding networks by coupling the use of extracted ion chromatograms (XICs) of cysteine-containing peptides with ETD analysis to produce an efficient assignment approach for disulfide bonding. This method can be used to assign a disulfide pattern in a de novo fashion, to detect disulfide shuffling, and to provide information on heterogeneity, when more than one disulfide bonding pattern is present. The method was applied for assigning the disulfide-bonding network of a recombinant monomer of the HIV envelope protein gp120. It was found that one region of the protein, the V1/V2 loops, had significant heterogeneity in the disulfide bonds.
Collapse
Affiliation(s)
- Daniel F Clark
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | | | | |
Collapse
|
32
|
Tan L, Durand KL, Ma X, Xia Y. Radical cascades in electron transfer dissociation (ETD) – implications for characterizing peptide disulfide regio-isomers. Analyst 2013; 138:6759-65. [DOI: 10.1039/c3an01333b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
33
|
Tan L, Xia Y. Gas-phase peptide sulfinyl radical ions: formation and unimolecular dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2011-2019. [PMID: 22911098 DOI: 10.1007/s13361-012-0465-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 06/01/2023]
Abstract
A variety of peptide sulfinyl radical (RSO•) ions with a well-defined radical site at the cysteine side chain were formed at atmospheric pressure (AP), sampled into a mass spectrometer, and investigated via collision-induced dissociation (CID). The radical ion formation was based on AP reactions between oxidative radicals and peptide ions containing single inter-chain disulfide bond or free thiol group generated from nanoelectrospray ionization (nanoESI). The radical induced reactions allowed large flexibility in forming peptide radical ions independent of ion polarity (protonated or deprotonated) or charge state (singly or multiply charged). More than 20 peptide sulfinyl radical ions in either positive or negative ion mode were subjected to low energy collisional activation on a triple-quadrupole/linear ion trap mass spectrometer. The competition between radical- and charge-directed fragmentation pathways was largely affected by the presence of mobile protons. For peptide sulfinyl radical ions with reduced proton mobility (i.e., singly protonated, containing basic amino acid residues), loss of 62 Da (CH(2)SO), a radical-initiated dissociation channel, was dominant. For systems with mobile protons, this channel was suppressed, while charge-directed amide bond cleavages were preferred. The polarity of charge was found to significantly alter the radical-initiated dissociation channels, which might be related to the difference in stability of the product ions in different ion charge polarities.
Collapse
Affiliation(s)
- Lei Tan
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
| | | |
Collapse
|
34
|
Li H, O'Connor PB. Electron capture dissociation of disulfide, sulfur-selenium, and diselenide bound peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2001-2010. [PMID: 22993041 DOI: 10.1007/s13361-012-0473-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/10/2012] [Accepted: 08/10/2012] [Indexed: 06/01/2023]
Abstract
To examine the electron capture dissociation (ECD) behavior of disulfide (S-S), sulfur-selenium (S-Se), and diselenide (Se-Se) bonds-containing peptides, a series of free cysteine (Cys) and selenocysteine (Sec) containing peptides were reacted to form interchain S-S, S-Se, and Se-Se bonds, and then studied using ECD with Fourier transform ion cyclotron mass spectrometry (FTICR MS). These results demonstrate that the radical has higher tendency to stay at selenium rather than sulfur after the cleavage of Se-S bonds by ECD. In addition, -SH (-33), -S (-32), and -S + H (-31) small neutral losses were all observed from the cleavage of C-S bonds of a disulfide bound peptide. Similar, but minor, fragments were also detected in S-Se bound peptides. In contrast, the cleavage of C-Se bonds of the Se-Se species mainly forms fragments with neutral loss of -Se + H (-78.90868), and the radical tends to stay on the selenium of its corresponding complementary pair. Although the electron affinities of S atom (2.07 eV) and Se atom (2.02 eV) are very close; they have very different reactivity towards electrons. The replacement of sulfur with selenium greatly increases the electron affinities of S-Se and Se-Se bonds comparing to S-S bonds (with an increase of electron affinity by about 0.20 eV by replacing a sulfur with a selenium) (Int J Quantum Chem 110:513-523, 2010), which in turn leads to different ECD fragmentation behavior and mechanisms. Our results are in good agreement with previously published ab initio calculations on Se-Se compounds by other groups.
Collapse
Affiliation(s)
- Huilin Li
- Department of Chemistry, University of Warwick, Coventry, UK
| | | |
Collapse
|
35
|
Kim JS, Song JS, Kim Y, Park SB, Kim HJ. De novo analysis of protein N-terminal sequence utilizing MALDI signal enhancing derivatization with Br signature. Anal Bioanal Chem 2011; 402:1911-9. [PMID: 22200925 DOI: 10.1007/s00216-011-5642-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/29/2011] [Accepted: 12/06/2011] [Indexed: 11/24/2022]
Abstract
De novo analysis of protein N-terminal sequence is important for identification of N-terminal proteolytic processing such as N-terminal methionine or signal peptide removal, or for the genome annotation of uncharacterized proteins. We introduce a de novo sequencing method of protein N terminus utilizing matrix-assisted laser desorption/ionization (MALDI) signal enhancing picolinamidination with bromine isotopic tag incorporated to the N terminus. The doublet signature of bromine in the tandem mass (MS/MS) spectrum distinguished N-terminal ion series from C-terminal ion series, facilitating de novo N-terminal sequencing of protein. The dual advantage of MALDI signal enhancement by the basic picolinamidine and b-ion selection aided by Br signature is demonstrated using a variety of peptides. The N-terminal sequences of myoglobin and hemoglobin as model proteins were determined by incorporating the Br tag to the N terminus of the proteins and obtaining a series of b-ions with Br signature by MS/MS analysis after chymotryptic digestion of the tagged proteins. The N-terminal peptide was selected for MS/MS analysis from the chymotryptic digest based on the Br signature in the mass spectrum. Identification of phosphorylation site as well as N-terminal sequencing of a phosphopeptide was straightforward.
Collapse
Affiliation(s)
- Jong-Seo Kim
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea.
| | | | | | | | | |
Collapse
|