1
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DeFiglia SA, Szot CW, Håkansson K. Negative-Ion Electron Capture Dissociation of MALDI-Generated Peptide Anions. Anal Chem 2024; 96:8800-8806. [PMID: 38742421 DOI: 10.1021/acs.analchem.4c01292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Negative-ion electron capture dissociation (niECD) is an anion MS/MS technique that provides fragmentation analogous to conventional ECD, including high peptide sequence coverage and retention of labile post-translational modifications (PTMs). niECD has been proposed to be the most efficient for salt-bridged zwitterionic precursor ion structures. Several important PTMs, e.g., sulfation and phosphorylation, are acidic and can, therefore, be challenging to characterize in the positive-ion mode. Furthermore, PTM-friendly techniques, such as ECD, require multiple precursor ion-positive charges. By contrast, singly charged ions, refractory to ECD, are most compatible with niECD. Because electrospray ionization (ESI) typically yields multiply charged ions, we sought to explore matrix-assisted laser desorption/ionization (MALDI) in combination with niECD. However, the requirement for zwitterionic gaseous structures may preclude efficient niECD of MALDI-generated anions. Unexpectedly, we found that niECD of anions from MALDI is not only possible but proceeds with similar or higher efficiency compared with ESI-generated anions. Matrix selection did not appear to have a major effect. With MALDI, niECD is demonstrated up to m/z ∼4300. For such larger analytes, multiple electron captures are observed, resulting in triply charged fragments from singly charged precursor ions. Such charge-increased fragments show improved detectability. Furthermore, significantly improved (∼20-fold signal-to-noise increase) niECD spectral quality is achieved with equivalent sample amounts from MALDI vs ESI. Overall, the reported combination with MALDI significantly boosts the analytical utility of niECD.
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Affiliation(s)
- Steven A DeFiglia
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Carson W Szot
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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2
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Takayama M. Transient Conformations Leading to Peptide Fragment Ion [c + 2H] + via Intramolecular Hydrogen Bonding Using MALDI In-source Decay Mass Spectrometry of Serine-, Threonine-, and/or Cysteine-Containing Peptides. Molecules 2023; 28:7700. [PMID: 38067431 PMCID: PMC10708033 DOI: 10.3390/molecules28237700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The formation of a peptide fragment ion [c + 2H]+ was examined using ultraviolet matrix-assisted laser desorption/ionization in-source decay mass spectrometry (UV/MALDI-ISD MS). Unusually, an ISD experiment with a hydrogen-abstracting oxidative matrix 4-nitro-1-naphthol (4,1-NNL) resulted in a [c + 2H]+ ion when the analyte peptides contained serine (Ser), threonine (Thr), and/or cysteine (Cys) residues, although the ISD with 4,1-NNL merely resulted in [a]+ and [d]+ ions. The [c + 2H]+ ion observed could be rationalized through intramolecular hydrogen atom transfer (HAT), like a Type-II reaction via a seven-membered conformation involving intramolecular hydrogen bonding (HB) between the active hydrogens (-OH and -SH) of the Ser/Thr/Cys residues and the backbone carbonyl oxygen at the adjacent amino (N)-terminal side residue. The ISD of the Cys-containing peptide resulted in the [c + 2H]+ ions, which originated from cleavage at the backbone N-Cα bonds far from the Cys residue, suggesting that the peptide molecule formed 16- and 22-membered transient conformations in the gas phase. The time-dependent density functional theory (TDDFT) calculations of the model structures of the Ser and Cys residues indicated that the Cys residue did not show a constructive bond interaction between the donor thiol (-SH) and carbonyl oxygen (=CO), while the Ser residue formed a distinct intramolecular HB.
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Affiliation(s)
- Mitsuo Takayama
- Graduate School in Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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3
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Jiang R, Rempel DL, Gross ML. Toward a MALDI in-source decay (ISD) method for top-down analysis of protein footprinting. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:292-302. [PMID: 37750197 PMCID: PMC11092977 DOI: 10.1177/14690667231202695] [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: 09/27/2023]
Abstract
Irreversible protein footprinting is a mass spectrometry-based approach in which solvent-accessible sites of a protein are modified to assess high-order protein structure. Structural insights can be gained by determining the position and extents of modification. The usual approach to obtain the "footprint" is to analyze the protein through bottom-up LC-MS/MS. In this approach, the proteins are digested to yield a mixture of peptides that are then separated by LC before locating the modification sites by MS/MS. This process consumes substantial amounts of time and is difficult to accelerate for applications that require quick and high-throughput analysis. Here, we describe employing matrix-assisted laser desorption/ionization (MALDI) in-source decay (ISD) to analyze a footprinted small test protein (ubiquitin) via a top-down approach. Matrix-assisted laser desorption/ionization is easily adapted for high-throughput analysis, and top-down strategies can avoid lengthy proteolysis and LC separation. We optimized the method with model peptides and then demonstrated its feasibility on ubiquitin submitted to two types of footprinting. We found that MALDI ISD can produce a comprehensive set of fragment ions for small proteins, affording footprinting information in a fast manner and giving results that agree with the established methods, and serve as a rough measure of protein solvent accessibility. To assist in the implementation of the MALDI approach, we developed a method of processing top-down ISD data.
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Affiliation(s)
- Ruidong Jiang
- Department of Chemistry, Washington University in St Louis, St Louis, MO, USA
| | - Don L Rempel
- Department of Chemistry, Washington University in St Louis, St Louis, MO, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St Louis, St Louis, MO, USA
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4
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Ni Z, Arevalo R, Bardyn A, Willhite L, Ray S, Southard A, Danell R, Graham J, Li X, Chou L, Briois C, Thirkell L, Makarov A, Brinckerhoff W, Eigenbrode J, Junge K, Nunn BL. Detection of Short Peptides as Putative Biosignatures of Psychrophiles via Laser Desorption Mass Spectrometry. ASTROBIOLOGY 2023; 23:657-669. [PMID: 37134219 DOI: 10.1089/ast.2022.0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Studies of psychrophilic life on Earth provide chemical clues as to how extraterrestrial life could maintain viability in cryogenic environments. If living systems in ocean worlds (e.g., Enceladus) share a similar set of 3-mer and 4-mer peptides to the psychrophile Colwellia psychrerythraea on Earth, spaceflight technologies and analytical methods need to be developed to detect and sequence these putative biosignatures. We demonstrate that laser desorption mass spectrometry, as implemented by the CORALS spaceflight prototype instrument, enables the detection of protonated peptides, their dimers, and metal adducts. The addition of silicon nanoparticles promotes the ionization efficiency, improves mass resolving power and mass accuracies via reduction of metastable decay, and facilitates peptide de novo sequencing. The CORALS instrument, which integrates a pulsed UV laser source and an Orbitrap™ mass analyzer capable of ultrahigh mass resolving powers and mass accuracies, represents an emerging technology for planetary exploration and a pathfinder for advanced technique development for astrobiological objectives. Teaser: Current spaceflight prototype instrument proposed to visit ocean worlds can detect and sequence peptides that are found enriched in at least one strain of microbe surviving in subzero icy brines via silicon nanoparticle-assisted laser desorption analysis.
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Affiliation(s)
- Ziqin Ni
- University of Maryland, College Park, Maryland, USA
| | | | - Anais Bardyn
- University of Maryland, College Park, Maryland, USA
| | | | - Soumya Ray
- University of Maryland, College Park, Maryland, USA
| | | | - Ryan Danell
- Danell Consulting, Winterville, North Carolina, USA
| | - Jacob Graham
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Xiang Li
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Georgetown University, Washington, DC, USA
| | - Christelle Briois
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace, Orléans, France
| | - Laurent Thirkell
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace, Orléans, France
| | | | | | | | - Karen Junge
- University of Washington, Seattle, Washington, USA
| | - Brook L Nunn
- University of Washington, Seattle, Washington, USA
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5
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Liew CY, Chen JL, Ni CK. Electrospray ionization in-source decay of N-glycans and the effects on N-glycan structural identification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9352. [PMID: 35830282 DOI: 10.1002/rcm.9352] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
RATIONAL Electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) are soft ionization techniques commonly used in mass spectrometry. Although in-source and post-source decays of MALDI have been investigated extensively, the analogous decays of ESI have received little attention. Previous studies regarding the analogous decays of ESI focus on the dissociation of multiply charged proteins and peptides. The decay of carbohydrates in ESI has not been investigated yet, and it may have interference in carbohydrate structural determination. METHODS Commercial apparatus, including a high-performance liquid chromatography (HPLC), an ESI source, and a linear ion trap mass spectrometer, were used to investigate the fragmentation of several N-glycans during the ESI process. RESULTS About 0.2%-3% of neutral N-glycans and more than 50% of N-glycans consisting of a sialic acid are dissociated into small N-glycans by ESI in-source decay in typical ESI operating conditions. The efficiencies of most dissociation channels increase as the temperature of ion transfer capillary increases, indicating that part of the energy deposited into the precursor ions for cracking is from the heated capillary. The cracking patterns of ESI in-source decay are slightly different from those of gaseous phase collision-induced dissociation. CONCLUSIONS Large N-glycans are dissociated into small N-glycans in ESI in-source decay that may result in the interference of the structural identification of small N-glycans. Separation of large N-glycans from small N-glycans, for example, using HPLC, prior to ESI ionization is necessary to eliminate the interference. This is particularly important when N-glycans consist of sialic acid or large N-glycans have much higher concentration than that of small N-glycans in ESI solution.
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Affiliation(s)
- Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei, Taiwan
| | - Jien-Lian Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
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6
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Chen SY, Zhou QYJ, Chen L, Li JY, Xie T, Zhang SH. Screening and identifying cucurbitacins and cucurbitacin glycosides in Cucumis sativus using high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry combined with in-source fragmentation and alkali adduct ions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9323. [PMID: 35560736 DOI: 10.1002/rcm.9323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/15/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
RATIONALE Cucumber, as a popular fruit and vegetable, has tremendously contributed to providing a sufficient and high-quality food supply. However, the cucumber plant metabolites, which may possess potential benefits for human health, were rarely reported. In addition, rapid detection of these metabolites from the complex biological matrix of cucumber samples is a tremendous challenge. METHODS A rapid detection method was established to systematically screen cucurbitacins and cucurbitacin glycosides in cucumber plants by combining high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (HPLC-Q-TOF-MS) with in-source fragmentation (ISF). Moreover, the alkali cations, including acetic acid, 0.1% LiCl, 0.1% NH4 Cl, 0.1% NaCl, and 0.1% KCl, were added to the mobile phase for improving the ion response. RESULTS The fragmentation pathways of seven cucurbitacins and cucurbitacin glycosides were primarily investigated. The characteristic ISF ions at m/z 501.3211 and 503.3367 were identified and employed to screen 40 cucurbitacins and cucurbitacin glycosides from the complex biological matrix. Their structures were identified by their tandem mass spectrometry (MS/MS) spectra and fragmentation pathways of references. Finally, the metabolic distribution and network of cucurbitacins and cucurbitacin glycosides in cucumber plants were also proposed. CONCLUSIONS This work marks the first systematic and comprehensive study of the metabolites in cucumber plants using HPLC-Q-TOF-MS technology, providing a template for screening and identifying the triterpenoids from other plant-derived medicines or food.
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Affiliation(s)
- Si-Yuan Chen
- The First Hospital of Hunan University of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Qing Yi-Jun Zhou
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Lin Chen
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Jia-Yu Li
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Tao Xie
- Department of Acupuncture and Rehabilitation, Changsha Traditional Chinese Medicine Hospital, Changsha, China
| | - Shui-Han Zhang
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
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7
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Asakawa D, Hosokai T, Nakayama Y. Experimental and Theoretical Investigation of MALDI In-Source Decay of Peptides with a Reducing Matrix: What Is the Initial Fragmentation Step? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1011-1021. [PMID: 35587880 DOI: 10.1021/jasms.2c00066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) with a reducing matrix is believed to be initiated by hydrogen transfer from the matrix to the peptide. Several new matrices have recently been developed to achieve more efficient MALDI-ISD. In particular, the use of matrices containing aniline groups facilitates MALDI-ISD to a greater extent than that of matrices containing phenol groups, although the N-H bond in aniline is stronger than the O-H bond in phenol. In this study, photoelectron yield spectroscopy of matrix solids revealed that conversion of the phenol group to the aniline group decreased the ionization energy of the matrix solids. Crucially, the use of a matrix with lower ionization energy has been found to result in efficient cleavage at N-Cα and disulfide bonds by MALDI-ISD. Therefore, electron association with the peptide rather than the fragmentation mechanism involving hydrogen atom attachment is proposed as the initial step of the MALDI-ISD process. In this mechanism, electron transfer from the reducing matrix to the peptide produces a peptide anion radical, which provides either a [cn + H]/[zm]• or [an]•/[ym + H] fragment pair. Fragmentation of the peptide anion radical strongly depends on the gas-phase acidity of the matrix used. Subsequently, the resultant fragments/radicals underwent a reaction in the MALDI plume, producing observable even-electron ions. Consequently, MALDI-ISD fragments are observed as both positive and negative ions, even though MALDI-ISD with a reducing matrix involves fragmentation of peptide anion radicals. The proposed mechanism is suitable for obtaining a better understanding of the MALDI-ISD process.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Takuya Hosokai
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
- Department of Pure and Applied Chemistry, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yasuo Nakayama
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
- Department of Pure and Applied Chemistry; Division of Colloid and Interface Science; Research Group for Advanced Energy Conversion, Tokyo University of Science, Noda 278-8510, Japan
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8
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Wang HYJ, Hsu FF. Structural characterization of phospholipids and sphingolipids by in-source fragmentation MALDI/TOF mass spectrometry. Anal Bioanal Chem 2022; 414:2089-2102. [PMID: 35013808 PMCID: PMC8882230 DOI: 10.1007/s00216-021-03843-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Phospholipids (PLs) and sphingolipids (SLs) perform critical structural and biological functions in cells. The structure of these lipids, including the stereospecificity and double-bond position of fatty acyl (FA) chains, is critical in decoding lipid biology. In this study, we presented a simple in-source fragmentation (ISF) MALDI/TOF mass spectrometry method that affords complete structural characterization of PL and SL molecules. We analyzed several representative unsaturated lipid species including phosphatidylcholine (PC), plasmalogen PC (pPC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), cardiolipin (CL), sphingomyelin (SM), and ceramide (Cer). Fragment ions reflecting the FA chains at sn-1 and sn-2 position, and those characteristics of the head groups of different PL classes, are readily identified. Specific fragment ions from cleavages of the C-C bond immediately adjacent to the cis C=C double-bond position(s) of FA chains and the trans C=C double bond of the sphingosine constituents allow precise localization of double bonds. The identities of the exemplary product ions from vinylic, allylic, and double-bond cleavages were also verified by LIFT-TOF/TOF. Identification of individual PL species in the lipid mixture was also carried out with ISF-MALDI/TOF. Together, this approach provides a simple yet effective method for structural characterization of PLs and SLs without the additional modification on the instrument hardware, and serves as a simple tool for the identification of lipids.
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Affiliation(s)
- Hay-Yan J Wang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan.
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Washington University School of Medicine, Box 8127, St. Louis, MO, 63110, USA.
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Washington University School of Medicine, Box 8127, St. Louis, MO, 63110, USA
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9
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Borbély A, Pethő L, Szabó I, Al-Majidi M, Steckel A, Nagy T, Kéki S, Kalló G, Csősz É, Mező G, Schlosser G. Structural Characterization of Daunomycin-Peptide Conjugates by Various Tandem Mass Spectrometric Techniques. Int J Mol Sci 2021; 22:ijms22041648. [PMID: 33562082 PMCID: PMC7914584 DOI: 10.3390/ijms22041648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 11/16/2022] Open
Abstract
The use of peptide-drug conjugates has generated wide interest as targeted antitumor therapeutics. The anthracycline antibiotic, daunomycin, is a widely used anticancer agent and it is often conjugated to different tumor homing peptides. However, comprehensive analytical characterization of these conjugates via tandem mass spectrometry (MS/MS) is challenging due to the lability of the O-glycosidic bond and the appearance of MS/MS fragment ions with little structural information. Therefore, we aimed to investigate the optimal fragmentation conditions that suppress the prevalent dissociation of the anthracycline drug and provide good sequence coverage. In this study, we comprehensively compared the performance of common fragmentation techniques, such as higher energy collisional dissociation (HCD), electron transfer dissociation (ETD), electron-transfer higher energy collisional dissociation (EThcD) and matrix-assisted laser desorption/ionization–tandem time-of-flight (MALDI-TOF/TOF) activation methods for the structural identification of synthetic daunomycin-peptide conjugates by high-resolution tandem mass spectrometry. Our results showed that peptide backbone fragmentation was inhibited by applying electron-based dissociation methods to conjugates, most possibly due to the “electron predator” effect of the daunomycin. We found that efficient HCD fragmentation was largely influenced by several factors, such as amino acid sequences, charge states and HCD energy. High energy HCD and MALDI-TOF/TOF combined with collision induced dissociation (CID) mode are the methods of choice to unambiguously assign the sequence, localize different conjugation sites and differentiate conjugate isomers.
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Affiliation(s)
- Adina Borbély
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group and Department of Analytical Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (A.B.); (M.A.-M.); (A.S.)
| | - Lilla Pethő
- Eötvös Loránd Research Network, Supported Research Groups, Research Group of Peptide Chemistry, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (L.P.); (I.S.); (G.M.)
| | - Ildikó Szabó
- Eötvös Loránd Research Network, Supported Research Groups, Research Group of Peptide Chemistry, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (L.P.); (I.S.); (G.M.)
| | - Mohammed Al-Majidi
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group and Department of Analytical Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (A.B.); (M.A.-M.); (A.S.)
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Arnold Steckel
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group and Department of Analytical Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (A.B.); (M.A.-M.); (A.S.)
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Tibor Nagy
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (S.K.)
| | - Sándor Kéki
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (S.K.)
| | - Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (G.K.); (É.C.)
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (G.K.); (É.C.)
| | - Gábor Mező
- Eötvös Loránd Research Network, Supported Research Groups, Research Group of Peptide Chemistry, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (L.P.); (I.S.); (G.M.)
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group and Department of Analytical Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (A.B.); (M.A.-M.); (A.S.)
- Correspondence: ; Tel.: +36-1-372-2500
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10
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Nicolardi S, Kilgour DPA, van der Burgt YEM, Wuhrer M. Improved N- and C-Terminal Sequencing of Proteins by Combining Positive and Negative Ion MALDI In-Source Decay Mass Spectrometry. Anal Chem 2020; 92:12429-12436. [PMID: 32803948 PMCID: PMC7498143 DOI: 10.1021/acs.analchem.0c02198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/17/2020] [Indexed: 01/10/2023]
Abstract
The development of various ionization and fragmentation techniques has been of key importance for establishing mass spectrometry (MS) as a powerful tool for protein characterization. One example of this is matrix-assisted laser desorption/ionization (MALDI) combined with in-source decay (ISD) fragmentation that allows mapping of N- and C-terminal regions of large proteins without the need for proteolysis. Positive ion mode ISD fragments are commonly assigned in the mass region above m/z 1000, while MALDI matrix ions generally hamper the detection of smaller singly charged fragments. The ultrahigh resolving power provided by Fourier transform ion cyclotron resonance (FT-ICR) MS partially overcomes this limitation, but to further increase the detection of smaller fragments we have revisited the application of negative ion mode MALDI-ISD and found good coverage of the peptide chain termini starting from c'2 and z'2 fragment ions. For the first time, we demonstrate that the combination of negative and positive ion MALDI FT-ICR MS is a useful tool to improve the characterization of mAbs. The different specificities of the two ion modes allowed us to selectively cover the sequence of the light and heavy chains of mAbs at increased sensitivity. A comprehensive evaluation of positive and negative ion mode MALDI-ISD FT-ICR MS in the m/z range 46-13 500 showed an increased sequence coverage for three standard proteins, namely, myoglobin, SiLuLite mAb, and NIST mAb. The data obtained in the two ion modes were, in part, complementary.
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Affiliation(s)
- Simone Nicolardi
- Center
for Proteomics & Metabolomics, Leiden
University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - David P. A. Kilgour
- Department
of Chemistry, Nottingham Trent University, Nottingham NG11 0JN, U.K.
| | - Yuri E. M. van der Burgt
- Center
for Proteomics & Metabolomics, Leiden
University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Manfred Wuhrer
- Center
for Proteomics & Metabolomics, Leiden
University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
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11
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Kumar S, Venkatesha MA, Lall S, Prakash S, Balaram P. Mechanistic Insights into an Unusual Side-Chain-Mediated N-C α Bond Cleavage under Collision-Induced Dissociation Conditions in the Disulfide-Containing Peptide Conopressin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1083-1092. [PMID: 32175740 DOI: 10.1021/jasms.0c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Conopressin, a nonapeptide disulfide CFIRNCPKG amide present in cone snail venom, undergoes a facile cleavage at the Cys6-Pro7 peptide bond to yield a disulfide bridged b6 ion. Analysis of the mass spectral fragmentation pattern reveals the presence of a major fragment ion, which is unambiguously assigned as the tripeptide sequence IRN amide. The sequence dependence of this unusual fragmentation process has been investigated by comparing it with the fragmentation patterns of related peptides, oxytocin (CYIQNCPLG amide), Lys-vasopressin (CYFQNCPKG amide), and a series of synthetic analogues. The results establish the role of the Arg4 residue in facilitating the unusual N-Cα bond cleavage at Cys6. Structures are proposed for a modified disulfide bridged fragment containing the Cys1 and Cys6 residues. Gas-phase molecular dynamics simulations provide evidence for the occurrence of conformational states that permit close approach of the Arg4 side chain to the Cys6 Cβ methylene protons.
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Affiliation(s)
- Sanjeev Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - M Achanna Venkatesha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sahil Lall
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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12
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Nicolardi S, Kilgour DPA, Dolezal N, Drijfhout JW, Wuhrer M, van der Burgt YEM. Evaluation of Sibling and Twin Fragment Ions Improves the Structural Characterization of Proteins by Top-Down MALDI In-Source Decay Mass Spectrometry. Anal Chem 2020; 92:5871-5881. [PMID: 32212639 PMCID: PMC7178258 DOI: 10.1021/acs.analchem.9b05683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Comprehensive determination
of primary sequence and identification
of post-translational modifications (PTMs) are key elements in protein
structural analysis. Various mass spectrometry (MS) based fragmentation
techniques are powerful approaches for mapping both the amino acid
sequence and PTMs; one of these techniques is matrix-assisted laser
desorption/ionization (MALDI), combined with in-source decay (ISD)
fragmentation and Fourier-transform ion cyclotron resonance (FT-ICR)
MS. MALDI-ISD MS protein analysis involves only minimal sample preparation
and does not require spectral deconvolution. The resulting MALDI-ISD
MS data is complementary to electrospray ionization-based MS/MS sequencing
readouts, providing knowledge on the types of fragment ions is available.
In this study, we evaluate the isotopic distributions of z′ ions in protein top-down MALDI-ISD FT-ICR mass spectra and
show why these distributions can deviate from theoretical profiles
as a result of co-occurring and isomeric z and y-NH3 ions. Two synthetic peptides, containing
either normal or deuterated alanine residues, were used to confirm
the presence and unravel the identity of isomeric z and y-NH3 fragment ions (“twins”).
Furthermore, two reducing MALDI matrices, namely 1,5-diaminonaphthalene
and N-phenyl-p-phenylenediamine
were applied that yield ISD mass spectra with different fragment ion
distributions. This study demonstrates that the relative abundance
of isomeric z and y-NH3 ions requires consideration for accurate and confident assignments
of z′ ions in MALDI-ISD FT-ICR mass spectra.
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Affiliation(s)
- Simone Nicolardi
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
| | - David P A Kilgour
- Department of Chemistry, Nottingham Trent University, Nottingham NG11 0JN, United Kingdom
| | - Natasja Dolezal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
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13
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Kimura S, Fujisaka A, Obika S. Nucleobase derivatives induce in-source decay of oligonucleotides as new matrix-assisted laser desorption/ionization matrices. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8620. [PMID: 31658399 DOI: 10.1002/rcm.8620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE For quality control of oligonucleotide therapeutics, accurate and efficient structural characterization using mass spectrometry techniques, such as liquid chromatography/mass spectrometry (LC/MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), is essential. In MALDI MS analysis, matrix selection is critical and a new matrix could enable more efficient and rapid structural analysis. METHODS We hypothesized that nucleobase derivatives could act as matrices more efficiently than the currently used matrices for oligonucleotides because of structural similarity, which leads to close contact with the analyte. To evaluate their suitability as matrices, 16 nucleobase derivatives were selected and tested as matrix candidates for oligonucleotide analysis. RESULTS Six of the 16 nucleobase derivatives acted as matrices for oligonucleotides. Particularly, 6-thioguanine (TG) performed well and induced clear in-source decay fragmentation. When TG or 2-amino-6-chloropurine was used as the matrix, oligonucleotides were ionized, and mainly the w and d fragment ions were observed. CONCLUSIONS Herein we demonstrate that a 10-mer RNA or DNA sequence can be successfully characterized using TG as matrix and suggest the possibility of using nucleobase derivatives as novel matrices in oligonucleotide sequencing.
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Affiliation(s)
- Satoshi Kimura
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Aki Fujisaka
- Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-Kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
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14
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Hempel BF, Damm M, Mrinalini, Göçmen B, Karış M, Nalbantsoy A, Kini RM, Süssmuth RD. Extended Snake Venomics by Top-Down In-Source Decay: Investigating the Newly Discovered Anatolian Meadow Viper Subspecies, Vipera anatolica senliki. J Proteome Res 2020; 19:1731-1749. [PMID: 32073270 DOI: 10.1021/acs.jproteome.9b00869] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we report on the venom proteome of Vipera anatolica senliki, a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and top-down proteomics analyses, were applied to fully characterize the venom of V. a. senliki. Furthermore, the classical top-down venomics approach was extended to elucidate the venom proteome by an alternative in-source decay (ISD) proteomics workflow using the reducing matrix 1,5-diaminonaphthalene. Top-down ISD proteomics allows for disulfide bond counting and effective de novo sequencing-based identification of high-molecular-weight venom constituents, both of which are difficult to achieve by commonly established top-down approaches. Venom gland transcriptome analysis identified 96 toxin transcript annotations from 18 toxin families. Relative quantitative snake venomics revealed snake venom metalloproteinases (42.9%) as the most abundant protein family, followed by several less dominant toxin families. Online mass profiling and top-down venomics provide a detailed insight into the venom proteome of V. a. senliki and facilitate a comparative analysis of venom variability for the closely related subspecies, Vipera anatolica anatolica.
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Affiliation(s)
- Benjamin-Florian Hempel
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Maik Damm
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Mrinalini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Bayram Göçmen
- Department of Biology, Faculty of Science, Ege University, 35100 Bornova, 35100 Izmir, Turkey
| | - Mert Karış
- Department of Biology, Faculty of Science, Ege University, 35100 Bornova, 35100 Izmir, Turkey
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Izmir, Bornova, Turkey
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16, Medical Drive, Singapore 117600
| | - Roderich D Süssmuth
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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15
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Asakawa D. General Mechanism of C α-C Peptide Backbone Bond Cleavage in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mediated by Hydrogen Abstraction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1491-1502. [PMID: 31147890 DOI: 10.1007/s13361-019-02214-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Nitrogen-centered and β-carbon-centered hydrogen-deficient peptide radicals are considered to be intermediates in the matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD)-induced Cα-C bond cleavage of peptide backbones when using an oxidizing matrix. To understand the general mechanism of Cα-C bond cleavage by MALDI-ISD, I study the fragmentation of model peptides and investigate the fragment formation pathways using calculations with density functional theory and transition state theory. The calculations indicate that the nitrogen-centered radical immediately undergoes Cα-C bond cleavage, leading to the formation of an a•/x fragment pair. In contrast, the dissociation of the β-carbon-centered radical is kinetically feasible under MALDI-ISD conditions, leading to the formation of an a/x• fragment pair. To discriminate these processes, I focus on the yield of d fragments, which originate from a• radicals through radical-induced side-chain loss, not from a fragments. The Cα-C bond cleavage on the C-terminal side of the carbamidomethylated cysteine residue is found to produce d fragments instead of a fragments. According to the calculation of the rate constant, the corresponding fragmentation occurs within 1 ns. The intense signal arising from d fragments and the lack of or weak signal from a fragments strongly suggest that the Cα-C bond cleavage occurs through a nitrogen-centered radical intermediate. In addition to the side-chain loss, the resulting a• radical undergoes hydrogen atom abstraction by the matrix. The results for a deuterium-labeled peptide indicate that the matrix abstracts a hydrogen atom from either the amide nitrogen or the β-carbon.
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Affiliation(s)
- Daiki Asakawa
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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16
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Sacks CD, Stumpo KA. Gold nanoparticles for enhanced ionization and fragmentation of biomolecules using LDI-MS. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1070-1077. [PMID: 30107051 DOI: 10.1002/jms.4282] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 06/08/2023]
Abstract
New applications for gold nanoparticles (AuNPs) in laser desorption ionization mass spectrometry are presented here. This work expands on previous biomolecule studies and introduces carbohydrates, steroids, bile acids, and other small molecules as a focus. Broad trends in ionization are observed, and specifically of interest are new species that have not previously been reported from AuNPs (e.g., [M + Au]+ ). Interesting fragmentation effects have been observed for diphenhydramine, including similarity to electron impact mass spectra and possible radical driven reactions, providing insight into the mechanism of ionization when using AuNPs.
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Affiliation(s)
- Cody D Sacks
- Department of Chemistry, University of Scranton, Scranton, PA, 18510, USA
| | - Katherine A Stumpo
- Department of Chemistry, University of Scranton, Scranton, PA, 18510, USA
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17
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OHTSU S, YAMAGUCHI M, NISHIWAKI H, FUKUSAKI E, SHIMMA S. Development of a Visualization Method for Imidacloprid in Drosophila melanogaster via Imaging Mass Spectrometry. ANAL SCI 2018; 34:991-996. [DOI: 10.2116/analsci.18scp04] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Seitaro OHTSU
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | | | - Hisashi NISHIWAKI
- Department of Bioscience, Graduate School of Agriculture, Ehime University
| | - Eiichiro FUKUSAKI
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Shuichi SHIMMA
- Department of Biotechnology, Graduate School of Engineering, Osaka University
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18
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Asakawa D, Takahashi H, Iwamoto S, Tanaka K. De Novo Sequencing of Tryptic Phosphopeptides Using Matrix-Assisted Laser Desorption/Ionization Based Tandem Mass Spectrometry with Hydrogen Atom Attachment. Anal Chem 2018; 90:2701-2707. [DOI: 10.1021/acs.analchem.7b04635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Daiki Asakawa
- National
Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hidenori Takahashi
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Koichi Tanaka
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto, 604-8511, Japan
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19
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Li P, Kreft I, Jackson GP. Top-Down Charge Transfer Dissociation (CTD) of Gas-Phase Insulin: Evidence of a One-Step, Two-Electron Oxidation Mechanism. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:284-296. [PMID: 28786096 PMCID: PMC5803485 DOI: 10.1007/s13361-017-1700-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 05/03/2023]
Abstract
Top-down analyses of protonated insulin cations of charge states of 4+, 5+, or 6+ were performed by exposing the isolated precursor ions to a beam of helium cations with kinetic energy of more than 6 keV, in a technique termed charge transfer dissociation (CTD). The ~100 ms charge transfer reaction resulted in approximately 20% conversion efficiency to other intact charge exchange products (CTnoD), and a range of low abundance fragment ions. To increase backbone and sulfide cleavages, and to provide better structural information than straightforward MS2 CTD, the CTnoD oxidized products were isolated and subjected to collisional activation at the MS3 level. The MS3 CTD/CID reaction effectively broke the disulfide linkages, separated the two chains, and yielded more structurally informative fragment ions within the inter-chain cyclic region. CTD also provided doubly oxidized intact product ions at the MS2 level, and resonance ejection of the singly oxidized product ion revealed that the doubly oxidized product originates directly from the isolated precursor ion and not from consecutive CTD reactions of a singly oxidized intermediate. MS4 experiments were employed to help identify potential radical cations and diradical cations, but the results were negative or inconclusive. Nonetheless, the two-electron oxidation process is a demonstration of the very large potential energy (>20 eV) available through CTD, and is a notable capability for a 3D ion trap platform. Graphical Abstract ᅟ.
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Affiliation(s)
- Pengfei Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Iris Kreft
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506-6121, USA
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506-6121, USA.
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20
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Medeiros AFD, Costa IDS, Carvalho FMCD, Kiyota S, Souza BBPD, Sifuentes DN, Serquiz RP, Maciel BLL, Uchôa AF, Santos EAD, Morais AHDA. Biochemical characterisation of a Kunitz-type inhibitor from Tamarindus indica L. seeds and its efficacy in reducing plasma leptin in an experimental model of obesity. J Enzyme Inhib Med Chem 2018; 33:334-348. [PMID: 29322840 PMCID: PMC6010142 DOI: 10.1080/14756366.2017.1419220] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A trypsin inhibitor isolated from tamarind seed (TTI) has satietogenic effects in animals, increasing the cholecystokinin (CCK) in eutrophy and reducing leptin in obesity. We purified TTI (pTTI), characterised, and observed its effect upon CCK and leptin in obese Wistar rats. By HPLC, and after amplification of resolution, two protein fractions were observed: Fr1 and Fr2, with average mass of [M + 14H]+ = 19,594,690 Da and [M + 13H]+ = 19,578,266 Da, respectively. The protein fractions showed 54 and 53 amino acid residues with the same sequence. pTTI presented resistance to temperature and pH variations; IC50 was 2.7 × 10−10 mol.L−1 and Ki was 2.9 × 10−11 mol.L−1. The 2-DE revealed spots with isoelectric points between pH 5 and 6, and one near pH 8. pTTI action on leptin decrease was confirmed. We conclude that pTTI is a Kunitz trypsin inhibitor with possible biotechnological health-related application.
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Affiliation(s)
- Amanda Fernandes de Medeiros
- a Postgraduate Biochemistry Program, Biosciences Center , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Izael de Sousa Costa
- a Postgraduate Biochemistry Program, Biosciences Center , Federal University of Rio Grande do Norte , Natal , Brazil
| | | | - Sumika Kiyota
- b Laboratory of Protein and Peptide Biochemistry , CPDSA, Biological Institute , São Paulo , Brazil
| | - Beatriz Blenda Pinheiro de Souza
- c Postgraduate Biological Molecular, Institute of Biological Sciences , University of Brasília , Distrito Federal , Brasília , Brazil.,d Embrapa Genetic Resources and Biotechnology , Embrapa , Distrito Federal , Brasília , Brazil
| | | | - Raphael Paschoal Serquiz
- a Postgraduate Biochemistry Program, Biosciences Center , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Bruna Leal Lima Maciel
- e Postgraduate Nutrition Program, Center for Health Sciences , Federal University of Rio Grande do Norte , Natal , Brazil.,f Department of Nutrition, Center for Health Sciences , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Adriana Ferreira Uchôa
- a Postgraduate Biochemistry Program, Biosciences Center , Federal University of Rio Grande do Norte , Natal , Brazil.,g Department of Cell Biology and Genetics, Biosciences Center , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Elizeu Antunes Dos Santos
- a Postgraduate Biochemistry Program, Biosciences Center , Federal University of Rio Grande do Norte , Natal , Brazil.,h Department of Biochemistry, Biosciences Center , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Ana Heloneida de Araújo Morais
- a Postgraduate Biochemistry Program, Biosciences Center , Federal University of Rio Grande do Norte , Natal , Brazil.,e Postgraduate Nutrition Program, Center for Health Sciences , Federal University of Rio Grande do Norte , Natal , Brazil.,f Department of Nutrition, Center for Health Sciences , Federal University of Rio Grande do Norte , Natal , Brazil
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21
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Qi Y, Müller MJ, Volmer DA. Activation of Reactive MALDI Adduct Ions Enables Differentiation of Dihydroxylated Vitamin D Isomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2532-2537. [PMID: 28842822 DOI: 10.1007/s13361-017-1775-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Vitamin D compounds are secosteroids, which are best known for their role in bone health. More recent studies have shown that vitamin D metabolites and catabolites such as dihydroxylated species (e.g., 1,25- and 24,25-dihydroxyvitamin D3) play key roles in the pathologies of various diseases. Identification of these isomers by mass spectrometry is challenging and currently relies on liquid chromatography, as the isomers exhibit virtually identical product ion spectra under collision induced dissociation conditions. Here, we developed a simple MALDI-CID method that utilizes ion activation of reactive analyte/matrix adducts to distinguish isomeric dihydroxyvitamin D3 species, without the need for chromatography separation or chemical derivatization techniques. Specifically, reactive 1,5-diaminonaphthalene adducts of dihydroxyvitamin D3 compounds formed during MADI were activated and specific cleavages in the secosteroid's backbone structure were achieved that produced isomer-diagnostic fragment ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Yulin Qi
- Institute of Bioanalytical Chemistry, Saarland University, D-66123, Saarbrücken, Germany
| | - Miriam J Müller
- Institute of Bioanalytical Chemistry, Saarland University, D-66123, Saarbrücken, Germany
| | - Dietrich A Volmer
- Institute of Bioanalytical Chemistry, Saarland University, D-66123, Saarbrücken, Germany.
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22
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Wang J, Wang C, Han X. Enhanced coverage of lipid analysis and imaging by matrix-assisted laser desorption/ionization mass spectrometry via a strategy with an optimized mixture of matrices. Anal Chim Acta 2017; 1000:155-162. [PMID: 29289304 DOI: 10.1016/j.aca.2017.09.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 01/03/2023]
Abstract
In matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) analysis and imaging of lipids, comprehensive ionization of lipids simultaneously by a universal matrix is a very challenging problem. Ion suppression of readily ionizable lipids to others is common. To overcome this obstacle and enhance the coverage of MALDI MS analysis and imaging of lipids, we developed a novel strategy employing a mixture of matrices, each of which is capable of selective ionization of different lipid classes. Given that MALDI MS with either 9-aminoacridine (9-AA) or N-(1-naphthyl) ethylenediamine dihydrochloride (NEDC) yields weak in-source decay which is critical for analysis of complex biological samples and possesses orthogonal selectivity for ionization of lipid classes, we tested the mixtures of NEDC and 9-AA with different ratios for analysis of standard lipids and mouse brain lipid extracts. We determined 1.35 of NEDC/9-AA as an optimized molar ratio. It was demonstrated that an enhanced coverage with the optimized mixture was obtained, which enabled us to analyze and map all the major classes of phospholipids and sulfatide from either lipid extracts or tissue slides, respectively. We believe that this powerful novel strategy can enhance lipidomics analysis and MALDI MS imaging of lipids in a high-throughput and semi-quantitative fashion.
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Affiliation(s)
- Jianing Wang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, United States
| | - Chunyan Wang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, United States
| | - Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, United States.
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23
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Furuki K, Toyo'oka T, Yamaguchi H. A novel rapid analysis using mass spectrometry to evaluate downstream refolding of recombinant human insulin-like growth factor-1 (mecasermin). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1267-1278. [PMID: 28523846 DOI: 10.1002/rcm.7906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/28/2017] [Accepted: 05/14/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Mecasermin is used to treat elevated blood sugar as well as growth-hormone-resistant Laron-type dwarfism. Mecasermin isolated from inclusion bodies in extracts of E. coli must be refolded to acquire sufficient activity. However, there is no rapid analytical method for monitoring refolding during the purification process. METHODS We prepared mecasermin drug product, in-process samples during the oxidation of mecasermin, forced-reduced mecasermin, and aerially oxidized mecasermin after forced reduction. Desalted mecasermin samples were analyzed using MALDI-ISD. The peak intensity ratio of product to precursor ion was determined. The charge-state distribution (CSD) of mecasermin ions was evaluated using ESI-MS coupled with SEC-mode HPLC. The drift time and collision cross-sectional area (CCS) of mecasermin ions were evaluated using ESI-IMS-MS coupled with SEC-mode HPLC. RESULTS MALDI-ISD data, CSD values determined using ESI-MS, and the CCS acquired using ESI-IMS-MS revealed the relationship between the folded and unfolded proteoforms of forced-reduced mecasermin and aerially oxidized mecasermin with the free-SH:protein ratio of mecasermin drug product. The CCS area, which is determined using ESI-IMS-MS, provided proteoform information through rapid monitoring (<2 min) of in-process samples during the manufacture of mecasermin. CONCLUSIONS ESI-IMS-MS coupled with SEC-mode HPLC is a rapid and robust method for analyzing the free-SH:protein ratio of mecasermin that allows proteoform changes to be evaluated and monitored during the oxidation of mecasermin. ESI-IMS-MS is applicable as a process analytical technology tool for identifying the "critical quality attributes" and implementing "quality by design" for manufacturing mecasermin.
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Affiliation(s)
- Kenichiro Furuki
- Process Science Lab II, Biotechnology Labs, Astellas Pharma Inc., Ibaraki, Japan
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
| | - Toshimasa Toyo'oka
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
| | - Hideto Yamaguchi
- Process Science Lab II, Biotechnology Labs, Astellas Pharma Inc., Ibaraki, Japan
- Astellas Institute for Regenerative Medicine (AIRM), Astellas Pharma Inc., Marlborough, MA, USA
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Asakawa D, Osaka I. Direct MALDI-MS analysis of the disulfide bonds in peptide using thiosalicylic acid as a reactive matrix. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:127-131. [PMID: 28074602 DOI: 10.1002/jms.3906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 12/26/2016] [Accepted: 01/08/2017] [Indexed: 06/06/2023]
Abstract
The ability of a thiol-containing molecule, thiosalicylic acid (TSA), to function as a reactive matrix for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry analysis of peptides has been investigated. Although TSA has reducing characteristics, the use of TSA did not cause a reduction-induced MALDI in-source decay, probably because of the weak interactions between the thiol group in TSA and the carboxyl oxygen in the peptide. In contrast, when peptides containing disulfide bonds were analyzed by MALDI with TSA as the matrix, the disulfide bond was partially cleaved owing to the reaction with TSA, producing TSA-adducted peptides. The reaction between the disulfide bond and TSA was suggested to be occurred in solution. The comparison of the MALDI mass spectra obtained using conventional matrix and TSA allows us to count the number of disulfide bonds in the peptides. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- D Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - I Osaka
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1211, Japan
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25
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Ait-Belkacem R, Dilillo M, Pellegrini D, Yadav A, de Graaf EL, McDonnell LA. In-Source Decay and Pseudo-MS 3 of Peptide and Protein Ions Using Liquid AP-MALDI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2075-2079. [PMID: 27752913 PMCID: PMC5088222 DOI: 10.1007/s13361-016-1511-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/09/2016] [Accepted: 09/11/2016] [Indexed: 05/12/2023]
Abstract
Atmospheric pressure MALDI on a Q-Exactive instrument was optimized for in-source decay and pseudo-MS3. The dependence of AP-MALDI ISD on the MALDI liquid matrix was investigated for peptides and proteins. The liquid matrices enabled long-life ISD signal, and exhibited high fragment ion yield and signal stability. Extensive a-, b-, c-, y-, and z-type fragment series were observed depending on the matrix used but were most extensive with 2,5-DHB. Complete sequence coverage of small peptide and intact protein-terminus sequence tags were obtained and confirmed using HCD as a pseudo-MS3 method. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Pisa, Italy
| | - Davide Pellegrini
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
- Scuola Normale Superiore di Pisa, Pisa, Italy
| | | | | | - Liam A McDonnell
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy.
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
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26
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Parr MK, Montacir O, Montacir H. Physicochemical characterization of biopharmaceuticals. J Pharm Biomed Anal 2016; 130:366-389. [DOI: 10.1016/j.jpba.2016.05.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/26/2022]
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Boulicault JE, Alves S, Cole RB. Negative Ion MALDI Mass Spectrometry of Polyoxometalates (POMs): Mechanism of Singly Charged Anion Formation and Chemical Properties Evaluation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1301-1313. [PMID: 27142457 DOI: 10.1007/s13361-016-1400-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
MALDI-MS has been developed for the negative ion mode analysis of polyoxometalates (POMs). Matrix optimization was performed using a variety of matrix compounds. A first group of matrixes offers MALDI mass spectra containing abundant intact singly charged anionic adduct ions, as well as abundant in-source fragmentations at elevated laser powers. A relative ranking of the ability to induce POM fragmentation is found to be: DAN > CHCA > CNA > DIT> HABA > DCTB > IAA. Matrixes of a second group provide poorer quality MALDI mass spectra without observable fragments. Sample preparation, including the testing of salt additives, was performed to optimize signals for a model POM, POMc12, the core structure of which bears four negative charges. The matrix 9-cyanoanthracene (CNA) provided the best signals corresponding to singly charged intact POMc12 anions. Decompositions of these intact anionic species were examined in detail, and it was concluded that hydrogen radical-induced mechanisms were not prevalent, but rather that the observed prompt fragments originate from transferred energy derived from initial electronic excitation of the CNA matrix. Moreover, in obtained MALDI mass spectra, clear evidence of electron transfer to analyte POM species was found: a manifestation of the POMs ability to readily capture electrons. The affinity of polyanionic POMc12 toward a variety of cations was evaluated and the following affinity ranking was established: Fe(3+) > Al(3+) > Li(+) > Ga(3+) > Co(2+) > Cr(3+) > Cu(2+) > [Mn(2+), Mg(2+)] > [Na(+), K(+)]. Thus, from the available cationic species, specific adducts are preferentially formed, and evidence is given that these higher affinity POM complexes are formed in the gas phase during the early stages of plume expansion. Graphical Abstract ᅟ.
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Affiliation(s)
- Jean E Boulicault
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 place Jussieu, 75252, Paris Cedex 05, France
| | - Sandra Alves
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 place Jussieu, 75252, Paris Cedex 05, France
| | - Richard B Cole
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 place Jussieu, 75252, Paris Cedex 05, France.
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28
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Asakawa D. Principles of hydrogen radical mediated peptide/protein fragmentation during matrix-assisted laser desorption/ionization mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:535-556. [PMID: 25286767 DOI: 10.1002/mas.21444] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is a very easy way to obtain large sequence tags and, thereby, reliable identification of peptides and proteins. Recently discovered new matrices have enhanced the MALDI-ISD yield and opened new research avenues. The use of reducing and oxidizing matrices for MALDI-ISD of peptides and proteins favors the production of fragmentation pathways involving "hydrogen-abundant" and "hydrogen-deficient" radical precursors, respectively. Since an oxidizing matrix provides information on peptide/protein sequences complementary to that obtained with a reducing matrix, MALDI-ISD employing both reducing and oxidizing matrices is a potentially useful strategy for de novo peptide sequencing. Moreover, a pseudo-MS(3) method provides sequence information about N- and C-terminus extremities in proteins and allows N- and C-terminal side fragments to be discriminated within the complex MALDI-ISD mass spectrum. The combination of high mass resolution of a Fourier transform-ion cyclotron resonance (FTICR) analyzer and the software suitable for MALDI-ISD facilitates the interpretation of MALDI-ISD mass spectra. A deeper understanding of the MALDI-ISD process is necessary to fully exploit this method. Thus, this review focuses first on the mechanisms underlying MALDI-ISD processes, followed by a discussion of MALDI-ISD applications in the field of proteomics. © 2014 Wiley Periodicals, Inc., Mass Spec Rev 35:535-556, 2016.
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Affiliation(s)
- Daiki Asakawa
- Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
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29
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Moskovets E, Misharin A, Laiko V, Doroshenko V. A comparative study on the analytical utility of atmospheric and low-pressure MALDI sources for the mass spectrometric characterization of peptides. Methods 2016; 104:21-32. [DOI: 10.1016/j.ymeth.2016.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/19/2015] [Accepted: 02/16/2016] [Indexed: 11/16/2022] Open
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Gupta SL, Dhiman V, Jayasekharan T, Sahoo NK. Analysis of argentinated peptide complexes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: Peptide = oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, neurotensin. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1313-1322. [PMID: 27173113 DOI: 10.1002/rcm.7562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/11/2016] [Accepted: 03/12/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE The increased use of silver nanoparticles (AgNPs) for various biological applications, and over-expression of various peptide receptors in different tumors/cancer cells, necessitate the need for dedicated investigations on the intrinsic binding ability of Ag with various biologically important peptides for better understanding of AgNPs-peptide interactions and for the future development of contrasting agents as well as drugs for imaging/biomedical applications. METHODS The [M+(Ag)n ](+) complexes are prepared and characterized using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). RESULTS Silver complexes of the peptides [M+(Ag)n ](+) , where M = oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, and neurotensin, have been investigated for their intrinsic Ag(+) -binding ability. Unusual binding of up to seven Ag(+) with these small peptides is observed. The mass spectra show n = 1-5 for bombesin and somatostatin, n = 1-6 for bradykinin and arg(8) -vasopressin, and n = 1-7 for oxytocin and neurotensin. In addition, oxytocin and arg(8) -vasopressin show the formation of dimers and their complexes [M2 +(Ag)n ](+) with n = 1-8 and n = 1-5, respectively. The possible amino acid residues responsible for Ag(+) binding in each peptide have been identified on the basis of density functional theory (DFT)-calculated binding energy values of Ag(+) towards individual amino acids. CONCLUSIONS Mass spectrometric evidence indicates that the peptides, viz., oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, and neurotensin, show greater affinity for Ag(+) . Hence, they may be used as carriers for AgNPs in targeted drug delivery as well as an alternative for iodinated contrasting agents in dual energy X-ray imaging techniques. Radio-labeled Ag with these peptides can also be used in radio-pharmaceuticals for diagnostic and therapeutic applications. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Shyam L Gupta
- Atomic & Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Vikas Dhiman
- Atomic & Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - T Jayasekharan
- Atomic & Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - N K Sahoo
- Atomic & Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
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31
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Asakawa D, Smargiasso N, De Pauw E. Estimation of peptide N-Cα bond cleavage efficiency during MALDI-ISD using a cyclic peptide. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:323-327. [PMID: 27194516 DOI: 10.1002/jms.3748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) induces N-Cα bond cleavage via hydrogen transfer from the matrix to the peptide backbone, which produces a c'/z• fragment pair. Subsequently, the z• generates z' and [z + matrix] fragments via further radical reactions because of the low stability of the z•. In the present study, we investigated MALDI-ISD of a cyclic peptide. The N-Cα bond cleavage in the cyclic peptide by MALDI-ISD produced the hydrogen-abundant peptide radical [M + 2H](+) • with a radical site on the α-carbon atom, which then reacted with the matrix to give [M + 3H](+) and [M + H + matrix](+) . For 1,5-diaminonaphthalene (1,5-DAN) adducts with z fragments, post-source decay of [M + H + 1,5-DAN](+) generated from the cyclic peptide showed predominant loss of an amino acid with 1,5-DAN. Additionally, MALDI-ISD with Fourier transform-ion cyclotron resonance mass spectrometry allowed for the detection of both [M + 3H](+) and [M + H](+) with two (13) C atoms. These results strongly suggested that [M + 3H](+) and [M + H + 1,5-DAN](+) were formed by N-Cα bond cleavage with further radical reactions. As a consequence, the cleavage efficiency of the N-Cα bond during MALDI-ISD could be estimated by the ratio of the intensity of [M + H](+) and [M + 3H](+) in the Fourier transform-ion cyclotron resonance spectrum. Because the reduction efficiency of a matrix for the cyclic peptide cyclo(Arg-Gly-Asp-D-Phe-Val) was correlated to its tendency to cleave the N-Cα bond in linear peptides, the present method could allow the evaluation of the efficiency of N-Cα bond cleavage for MALDI matrix development. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Daiki Asakawa
- National Metrology Institute of Japan (NMIJ), Reserch Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Nicolas Smargiasso
- Chemistry Department and GIGA-R, Mass Spectrometry Laboratory, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Chemistry Department and GIGA-R, Mass Spectrometry Laboratory, University of Liège, Liège, Belgium
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32
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McMillen CL, Wright PM, Cassady CJ. Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:847-855. [PMID: 26864792 DOI: 10.1007/s13361-016-1345-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/15/2016] [Accepted: 01/16/2016] [Indexed: 06/05/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.
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Affiliation(s)
- Chelsea L McMillen
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Patience M Wright
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Chemistry, The University of Georgia, Athens, GA, 30602, USA
| | - Carolyn J Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA.
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Takahashi H, Sekiya S, Nishikaze T, Kodera K, Iwamoto S, Wada M, Tanaka K. Hydrogen Attachment/Abstraction Dissociation (HAD) of Gas-Phase Peptide Ions for Tandem Mass Spectrometry. Anal Chem 2016; 88:3810-6. [DOI: 10.1021/acs.analchem.5b04888] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hidenori Takahashi
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Sadanori Sekiya
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Takashi Nishikaze
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Kei Kodera
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Motoi Wada
- Graduate
School of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Koichi Tanaka
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
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34
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Takayama M. MALDI In-Source Decay of Protein: The Mechanism of c-Ion Formation. ACTA ACUST UNITED AC 2016; 5:A0044. [PMID: 27162707 DOI: 10.5702/massspectrometry.a0044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 02/22/2016] [Indexed: 02/05/2023]
Abstract
The in-source decay (ISD) phenomenon, the fragmentation at an N-Cα bond of a peptide backbone that occurs within several tens of nanoseconds in the ion-source in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), is discussed from the standpoints of the discovery and early publications dealing with MALDI-ISD, the formation of c-ions in energy-sudden desorption/ionization methods, the formation of radical species in a MALDI, model construction for ISD, and matrix materials that are suitable for use in MALDI-ISD. The formation of c-ions derived from peptides and proteins in MALDI-ISD can be rationalized by a mechanism involving intermolecular hydrogen transfer, denoted as the "Takayama's model" by De Pauw's group (Anal. Chem. 79: 8678-8685, 2007). It should be emphasized that the model for MALDI-ISD was constructed on the basis of X-ray crystallography and scanning probe microscopy (SPM) analyses of matrix crystals, as well as the use of isotopically-labelled peptides.
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Affiliation(s)
- Mitsuo Takayama
- Mass Spectrometry Laboratory, Graduate School of Nanobioscience, Yokohama City University
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35
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Nagoshi K, Inatomi K, Osaka I, Takayama M. Photochemical Reactions of Aminonaphthols Caused by Laser Desorption/Ionization. Mass Spectrom (Tokyo) 2016; 5:A0048. [DOI: 10.5702/massspectrometry.a0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/30/2016] [Indexed: 11/23/2022] Open
Affiliation(s)
- Keishiro Nagoshi
- Mass Spectrometry Laboratory, Graduate School of Nanobioscience, Yokohama City University
| | - Kazuma Inatomi
- Mass Spectrometry Laboratory, Graduate School of Nanobioscience, Yokohama City University
| | - Issey Osaka
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology
| | - Mitsuo Takayama
- Mass Spectrometry Laboratory, Graduate School of Nanobioscience, Yokohama City University
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Yu X, Sargaeva NP, Thompson CJ, Costello CE, Lin C. In-Source Decay Characterization of Isoaspartate and β-Peptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:101-109. [PMID: 26644780 PMCID: PMC4669973 DOI: 10.1016/j.ijms.2015.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Deamidation and the subsequent formation of isoaspartic acid (isoAsp) are common modifications of asparagine (Asn) residues in proteins. Differentiation of isoAsp and Asp residues is a challenging task owing to their similar chemical properties and identical molecular mass. Recent studies showed that they can be differentiated using electron capture dissociation (ECD) which generates diagnostic fragments c'+57 and z•-57 specific to the isoAsp residue. However, the ECD approach is only applicable towards multiply charged precursor ions and generally does not work for β-amino acids other than isoAsp. In this study, the potential of in-source decay (ISD) in characterization of isoAsp and other β-amino acids was explored. For isoAsp-containing peptides, ISD with a conventional hydrogen-donating matrix produced ECD-like, c'+57 and z•-57 diagnostic ions, even for singly charged precursor ions. For other β-amino acids, a hydrogen-accepting matrix was used to induce formation of site-specific a-14 ions from a synthetic β-analogue of substance P. These results indicated that ISD can be broadly applied for β-peptide characterization.
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Affiliation(s)
- Xiang Yu
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | - Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | | | - Catherine E. Costello
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
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37
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Théberge R, Dikler S, Heckendorf C, Chui DHK, Costello CE, McComb ME. MALDI-ISD Mass Spectrometry Analysis of Hemoglobin Variants: a Top-Down Approach to the Characterization of Hemoglobinopathies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1299-310. [PMID: 26002792 PMCID: PMC4496427 DOI: 10.1007/s13361-015-1164-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 05/13/2023]
Abstract
Hemoglobinopathies are the most common inherited disorders in humans and are thus the target of screening programs worldwide. Over the past decade, mass spectrometry (MS) has gained a more important role as a clinical means to diagnose variants, and a number of approaches have been proposed for characterization. Here we investigate the use of matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF MS) with sequencing using in-source decay (MALDI-ISD) for the characterization of Hb variants. We explored the effect of matrix selection using super DHB or 1,5-diaminonaphthalene on ISD fragment ion yield and distribution. MALDI-ISD MS of whole blood using super DHB simultaneously provided molecular weights for the alpha and beta chains, as well as extensive fragmentation in the form of sequence defining c-, (z + 2)-, and y-ion series. We observed sequence coverage on the first 70 amino acids positions from the N- and C-termini of the alpha and beta chains in a single experiment. An abundant beta chain N-terminal fragment ion corresponding to βc34 was determined to be a diagnostic marker ion for Hb S (β6 Glu→Val, sickle cell), Hb C (β6 Glu→Lys), and potentially for Hb E (β26 Glu→Lys). The MALDI-ISD analysis of Hb S and HbSC yielded mass shifts corresponding to the variants, demonstrating the potential for high-throughput screening. Characterization of an alpha chain variant, Hb Westmead (α122 His→Gln), generated fragments that established the location of the variant. This study is the first clinical application of MALDI-ISD MS for the determination and characterization of hemoglobin variants.
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Affiliation(s)
- Roger Théberge
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118
| | - Sergei Dikler
- Bruker Daltonics Inc., 40 Manning Road, Billerica, MA 01821
| | - Christian Heckendorf
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118
| | - David H. K. Chui
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118
| | - Mark E. McComb
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118
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38
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Nicolardi S, Switzar L, Deelder AM, Palmblad M, van der Burgt YE. Top-Down MALDI-In-Source Decay-FTICR Mass Spectrometry of Isotopically Resolved Proteins. Anal Chem 2015; 87:3429-37. [DOI: 10.1021/ac504708y] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Simone Nicolardi
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Linda Switzar
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - André M. Deelder
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Yuri E.M. van der Burgt
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
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39
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Moon JH, Yoon S, Bae YJ, Kim MS. Formation of gas-phase peptide ions and their dissociation in MALDI: insights from kinetic and ion yield studies. MASS SPECTROMETRY REVIEWS 2015; 34:94-115. [PMID: 24863621 DOI: 10.1002/mas.21427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/17/2014] [Indexed: 06/03/2023]
Abstract
Insights on mechanisms for the generation of gas-phase peptide ions and their dissociation in matrix-assisted laser desorption ionization (MALDI) gained from the kinetic and ion yield studies are presented. Even though the time-resolved photodissociation technique was initially used to determine the dissociation kinetics of peptide ions and their effective temperature, it was replaced by a simpler method utilizing dissociation yields from in-source decay (ISD) and post-source decay (PSD). The ion yields for a matrix and a peptide were measured by repeatedly irradiating a region on a sample and collecting ion signals until the sample in the region was completely depleted. Matrix- and peptide-derived gas-phase cations were found to be generated by pre-formed ion emission or by ion-pair emission followed by anion loss, but not by laser-induced ionization. The total number of ions, that is, matrix plus peptide, was found to be equal to the number of ions emitted from a pure matrix. A matrix plume was found to cool as it expanded, from around 800-1,000 K to 400-500 K. Dissociation of peptide ions along b/y channels was found to occur statistically, that is, following RRKM behavior. Small critical energy (E0 = 0.6-0.7 eV) and highly negative critical entropy (ΔS(‡) = -30 to -25 eu) suggested that the transition structure was stabilized by multiple intramolecular interactions.
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Affiliation(s)
- Jeong Hee Moon
- Medical Proteomics Research Center, KRIBB, Daejeon, 305-806, Korea
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40
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Bae YJ, Kim MS. A Thermal Mechanism of Ion Formation in MALDI. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:41-60. [PMID: 26161971 DOI: 10.1146/annurev-anchem-081413-024102] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An important recent discovery concerning the fundamentals of matrix-assisted laser desorption/ionization (MALDI) is that the abundance of each ion appearing in a spectrum is fixed, regardless of the experimental condition, when an effective temperature associated with the spectrum is fixed. We describe this phenomenon and the thermal picture for the ion formation in MALDI derived from it. Accepting that matrix-to-analyte proton transfer is in quasi-equilibrium as supported by experimental data, the above thermal determination occurs because the primary (matrix) ion formation processes are thermally governed. We propose that the abundances of the primary ions are limited by the autoprotolysis-recombination process regardless of how they are initially produced. Finally, we note that primary ion formation, secondary (analyte) ion formation, and their dissociations occur sequentially while the effective temperature of the matrix plume falls steadily due to cooling associated with expansion.
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Affiliation(s)
- Yong Jin Bae
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea;
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41
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Rand KD, Zehl M, Jørgensen TJD. Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling. Acc Chem Res 2014; 47:3018-27. [PMID: 25171396 DOI: 10.1021/ar500194w] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteins are dynamic molecules that exhibit conformational flexibility to function properly. Well-known examples of this are allosteric regulation of protein activity and ligand-induced conformational changes in protein receptors. Detailed knowledge of the conformational properties of proteins is therefore pertinent to both basic and applied research, including drug development, since the majority of drugs target protein receptors and a growing number of drugs introduced to the market are therapeutic peptides or proteins. X-ray crystallography provides a static picture at atomic resolution of the lowest-energy structure of the native ensemble. There is a growing need for sensitive analytical tools to explore all of the significant molecular structures in the conformational landscape of proteins. Hydrogen/deuterium exchange monitored by mass spectrometry (HDX-MS) has recently emerged as a powerful method for characterizing protein conformational dynamics. The basis of this method is the fact that backbone amides in stable hydrogen-bonded structures (e.g., α-helices and β-sheets) are protected against exchange with the aqueous solvent. All protein structures are dynamic, however, and eventually all of the protecting hydrogen bonds will transiently break as the protein--according to thermodynamic principles--cycles through partially unfolded states that correspond to excited free energy levels. As a result, all of the backbone amides will eventually become temporarily solvent-exposed and exchange-competent over time. Consequently, a folded protein in D2O will gradually incorporate deuterium into its backbone amides, and the kinetics of the process can be readily monitored by mass spectrometry. The deuterium uptake kinetics for the intact protein (global exchange kinetics) represents the sum of the exchange kinetics for the individual backbone amides. Local exchange kinetics is typically achieved by using pepsin digestion under quench conditions (i.e., under cold acidic conditions where the amide hydrogen exchange rate is slowed by many orders of magnitude). The ability to localize the individual deuterated residues (the spatial resolution) is determined by the size (typically ∼7-15 residues) and the number of peptic peptides. These peptides provide a relatively coarse-grained picture of the protein dynamics. A fundamental understanding of the relationship between protein function/dysfunction and conformational dynamics requires in many cases higher resolution and ultimately single-residue resolution. In this Account, we summarize our efforts to achieve single-residue deuterium levels in proteins by electron-based or laser-induced gas-phase fragmentation methods. A crucial analytical requirement for this approach is that the pattern of deuterium labeling from solution is retained in the gas-phase fragment ions. It is therefore essential to control and minimize any occurrence of gas-phase randomization of the solution deuterium label (H/D scrambling) during the MS experiment. For this purpose, we have developed model peptide probes to accurately measure the onset and extent of H/D scrambling. Our analytical procedures to control the occurrence of H/D scrambling are detailed along with the physical parameters that induce it during MS analysis. In light of the growing use of gas-phase dissociation experiments to measure the HDX of proteins in order to obtain a detailed characterization and understanding of the dynamic conformations and interactions of proteins at the molecular level, we discuss the perspectives and challenges of future high-resolution HDX-MS methodology.
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Affiliation(s)
- Kasper D. Rand
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Martin Zehl
- Department
of Pharmacognosy and Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark
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Asakawa D, Smargiasso N, De Pauw E. Coordination of alkali metal ions to model branched hexasaccharides dictates fragment yield in MALDI in-source decay with hydrogen abstraction using 5-nitrosalicylic acid as the matrix. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:1059-1062. [PMID: 25303396 DOI: 10.1002/jms.3415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/13/2014] [Accepted: 06/16/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Daiki Asakawa
- Department of Chemistry, Mass Spectrometry Laboratory and GIGA-R, University of Liege, Liege, 4000, Belgium
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Asakawa D, Smargiasso N, Quinton L, De Pauw E. Influences of proline and cysteine residues on fragment yield in matrix-assisted laser desorption/ionization in-source decay mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1040-1048. [PMID: 24700120 DOI: 10.1007/s13361-014-0868-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/20/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
Matrix-assisted laser desorption/ionization in-source decay produces highly informative fragments for the sequencing of peptides/proteins. Among amino acids, cysteine and proline residues were found to specifically influence the fragment yield. As they are both frequently found in small peptide structures for which de novo sequencing is mandatory, the understanding of their specific behaviors would allow useful fragmentation rules to be established. In the case of cysteine, a c•/w fragment pair originating from Xxx-Cys is formed by side-chain loss from the cysteine residue. The presence of a proline residue contributes to an increased yield of ISD fragments originating from N-Cα bond cleavage at Xxx1-Xxx2Pro, which is attributable to the cyclic structure of the proline residue. Our results suggest that the aminoketyl radical formed by MALDI-ISD generally induces the homolytic N-Cα bond cleavage located on the C-terminal side of the radical site. In contrast, N-Cα bond cleavage at Xxx-Pro produces no fragments and the N-Cα bond at the Xxx1-Xxx2Pro bond is alternatively cleaved via a heterolytic cleavage pathway.
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Affiliation(s)
- Daiki Asakawa
- Chemistry Department and GIGA-R, Mass Spectrometry Laboratory, University of Liege, Liege, Belgium,
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Access of hydrogen-radicals to the peptide-backbone as a measure for estimating the flexibility of proteins using matrix-assisted laser desorption/ionization mass spectrometry. Int J Mol Sci 2014; 15:8428-42. [PMID: 24828203 PMCID: PMC4057740 DOI: 10.3390/ijms15058428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/11/2014] [Accepted: 04/30/2014] [Indexed: 11/26/2022] Open
Abstract
A factor for estimating the flexibility of proteins is described that uses a cleavage method of “in-source decay (ISD)” coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The MALDI-ISD spectra of bovine serum albumin (BSA), myoglobin and thioredoxin show discontinuous intense ion peaks originating from one-side preferential cleavage at the N-Cα bond of Xxx-Asp, Xxx-Asn, Xxx-Cys and Gly-Xxx residues. Consistent with these observations, Asp, Asn and Gly residues are also identified by other flexibility measures such as B-factor, turn preference, protection and fluorescence decay factors, while Asp, Asn, Cys and Gly residues are identified by turn preference factor based on X-ray crystallography. The results suggest that protein molecules embedded in/on MALDI matrix crystals partly maintain α-helix and that the reason some of the residues are more susceptible to ISD (Asp, Asn, Cys and Gly) and others less so (Ile and Val) is because of accessibility of the peptide backbone to hydrogen-radicals from matrix molecules. The hydrogen-radical accessibility in MALDI-ISD could therefore be adopted as a factor for measuring protein flexibility.
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Asakawa D, Smargiasso N, De Pauw E. New approach for pseudo-MS(3) analysis of peptides and proteins via MALDI in-source decay using radical recombination with 1,5-diaminonaphthalene. Anal Chem 2014; 86:2451-7. [PMID: 24512348 DOI: 10.1021/ac403285b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Matrix-assisted laser desorption ionization in-source decay (MALDI-ISD) is a useful method for top-down sequencing of proteins and preferentially produces the c'/z(•) fragment pair. Subsequently, radical z(•) fragments undergo a variety of radical reactions. This work is focused on the chemical properties of the 1,5-diaminonaphthalene (1,5-DAN) adducts on z fragment ions (zn*), which are abundant in MALDI-ISD spectra. Postsource decay (PSD) of the zn* fragments resulted in specific peptide bond cleavage adjacent to the binding site of 1,5-DAN, leading to the preferential formation of y'n-1 fragments. The dominant loss of an amino acid with 1,5-DAN from zn* can be used in pseudo-MS(3) mode to identify the C-terminal side fragments from a complex MALDI-ISD spectrum or to determine missed cleavage residues using MALDI-ISD. Although the N-Cα bond at the N-terminal side of Pro is not cleaved by MALDI-ISD, pseudo-MS(3) via zn* can confirm the presence of a Pro residue.
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Affiliation(s)
- Daiki Asakawa
- Chemistry Department, Mass Spectrometry Laboratory and GIGA-R, University of Liege , 4000 Liege, Belgium
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47
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Wang W, Chen Z, Billiar TR, Stang MT, Gao W. The carboxyl-terminal amino acids render pro-human LC3B migration similar to lipidated LC3B in SDS-PAGE. PLoS One 2013; 8:e74222. [PMID: 24040206 PMCID: PMC3769297 DOI: 10.1371/journal.pone.0074222] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/30/2013] [Indexed: 11/18/2022] Open
Abstract
LC3 is widely used marker for macroautophagy assays. After translation pro-LC3 is processed by Atg4 to expose C-terminal glycine residue for downstream conjugation reactions to accomplish the conversion of LC3-I to LC3-II. SDS-PAGE based Western blot (Wb) is generally utilized to quantify LC3-II levels where the LC3-I band migrates slower than LC3-II. We found that pro-human LC3B migrated at similar rate as LC3B-II in SDS-PAGE. The carboxyl-terminal five amino acids, particularly Lysine122 and Leucine123 of human LC3B play a major role in the faster migration of unprocessed LC3B, rendering it indistinguishable from LC3B-II in Wb assays. The unique faster migration of unprocessed LC3B than LC3B-I is also revealed in mouse LC3B, rat LC3B and rat LC3 but not in human LC3C. Our findings for the first time define pro-LC3 migration patterns for LC3 family member from human, mouse and rat species in SDS-PAGE. These findings provide a reference for pro-LC3 band patterns when Atg4 function is inhibited.
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Affiliation(s)
- Wei Wang
- College of Animal Science and Veterinary Medicine, Jilin University, Jilin, China
| | - Zhixia Chen
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Timothy R. Billiar
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Michael T. Stang
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (WG); (MTS)
| | - Wentao Gao
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (WG); (MTS)
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Asakawa D, Calligaris D, Zimmerman TA, De Pauw E. In-source decay during matrix-assisted laser desorption/ionization combined with the collisional process in an FTICR mass spectrometer. Anal Chem 2013; 85:7809-17. [PMID: 23879863 DOI: 10.1021/ac401234q] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The type of ions detected after in-source decay (ISD) in a MALDI source differs according to the ion source pressure and on the mass analyzer used. We present the mechanism leading to the final ISD ions for a Fourier transform-ion cyclotron resonance mass spectrometer (FTICR MS). The MALDI ion source was operated at intermediate pressure to cool the resulting ions and increase their lifetime during the long residence times in the FTICR ion optics. This condition produces not only c', z', and w fragments, but also a, y', and d fragments. In particular, d ions help to identify isobaric amino acid residues present near the N-terminal amino acid. Desorbed ions collide with background gas during desorption, leading to proton mobilization from Arg residues to a less favored protonation site. As a result, in the case of ISD with MALDI FTICR, the influence of the Arg residue in ISD fragmentation is less straightforward than for TOF MS and the sequence coverage is thus improved. MALDI-ISD combined with FTICR MS appears to be a useful method for sequencing of peptides and proteins including discrimination of isobaric amino acid residues and site determination of phosphorylation. Additionally we also used new software for in silico elimination of MALDI matrix peaks from MALDI-ISD FTICR mass spectra. The combination of high resolving power of an FTICR analyzer and matrix subtraction software helps to interpret the low m/z region of MALDI-ISD spectra. Finally, several of these developed methods are applied in unison toward a MALDI ISD FTICR imaging experiment on mouse brain to achieve better results.
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Affiliation(s)
- Daiki Asakawa
- Mass Spectrometry Laboratory, Department of Chemistry, and GIGA-Research, University of Liège, B-4000 Liège (Sart-Tilman), Belgium.
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50
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Ahn SH, Park KM, Bae YJ, Kim MS. Efficient methods to generate reproducible mass spectra in matrix-assisted laser desorption ionization of peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:868-876. [PMID: 23595259 DOI: 10.1007/s13361-013-0612-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/01/2013] [Accepted: 03/06/2013] [Indexed: 06/02/2023]
Abstract
In our previous matrix-assisted laser desorption ionization (MALDI) studies of peptides, we found that their mass spectra were virtually determined by the effective temperature in the early matrix plume, Tearly, when samples were rather homogeneous. This empirical rule allowed acquisition of quantitatively reproducible spectra. A difficulty in utilizing this rule was the complicated spectral treatment needed to get Tearly. In this work, we found another empirical rule that the total number of particles hitting the detector, or TIC, was a good measure of the spectral temperature and, hence, selection of spectra with the same TIC resulted in reproducible spectra. We also succeeded in obtaining reproducible spectra throughout a measurement by controlling TIC near a preset value through feedback adjustment of laser pulse energy. Both TIC selection and TIC control substantially reduced the shot-to-shot spectral variation in a spot, spot-to-spot variation in a sample, and even sample-to-sample variation in MALDI using α-cyano-4-hydroxycinnamic acid or 2,5-dihydroxybenzoic acid as matrix. Based on the utilization of acquired data, TIC control was more efficient than TIC selection by an order of magnitude. Both techniques produced calibration curves with excellent linearity, suggesting their utility in quantification of peptides.
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Affiliation(s)
- Sung Hee Ahn
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
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