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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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2
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Akor CJ, Cassady CJ. In-Source Decay MALDI and High-Energy Collision-Induced Dissociation Mass Spectrometry of Alkali Metal-Adducted Underivatized Oligosaccharides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2594-2606. [PMID: 37812625 DOI: 10.1021/jasms.3c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
In-source decay (ISD) and high-energy collision-induced dissociation (HE-CID) were explored to provide structural information on alkali metal-adducted linear and stacked oligosaccharides (oligosaccharides with increased flexibility due to linkage type). These oligosaccharides include isomeric tetrasaccharides, maltoheptaose, and several human milk oligosaccharides (HMOs). Matrix-assisted laser desorption ionization (MALDI) ion production efficiency, as well as the product ion intensities, and the number of product ions formed in ISD and HE-CID of these oligosaccharides were influenced by the matrix, the ionic radius of the metal ion used for adduction, and the affinity of metal ions for specific functional groups in the oligosaccharides. 2,4,6-Trihydroxyacetophenone (THAP) was the best matrix for HE-CID of oligosaccharides, 4-dimethylaminobenzaldehyde (DMABA) worked best for ISD of tetrasaccharides and pentasaccharides, while 2,5-dihydroxybenzoic acid (DHB) was the best matrix for ISD and HE-CID of long chain oligosaccharides. In general, the number of product ions formed followed the trend Li+ > Na+ > K+ > Rb+ > Cs+, except for HMOs where Na+ ≥ Li+ > K+ > Rb+ > Cs+ occurred. The type of product ions formed and their intensities varied based on the position of the glycosidic bond linkage and the content of the monosaccharide. ISD and HE-CID produced diagnostic ions that could structurally differentiate isomers. Overall, HE-CID of alkali-metal adducted oligosaccharides produces intense glycosidic bond cleavages and low intensity cross-ring and internal cleavages. In contrast, ISD generates mainly cross-ring cleavages and internal cleavages at intensities higher than in HE-CID. In addition, ISD produced unique product ions that complement results from HE-CID.
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Affiliation(s)
- Chioma J Akor
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carolyn J Cassady
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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3
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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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4
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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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5
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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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6
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Meier-Credo J, Preiss L, Wüllenweber I, Resemann A, Nordmann C, Zabret J, Suckau D, Michel H, Nowaczyk MM, Meier T, Langer JD. Top-Down Identification and Sequence Analysis of Small Membrane Proteins Using MALDI-MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1293-1302. [PMID: 35758524 PMCID: PMC9264385 DOI: 10.1021/jasms.2c00102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Identification and sequence determination by mass spectrometry have become routine analyses for soluble proteins. Membrane proteins, however, remain challenging targets due to their hydrophobicity and poor annotation. In particular small membrane proteins often remain unnoticed as they are largely inaccessible to Bottom-Up proteomics. Recent advances in structural biology, though, have led to multiple membrane protein complex structures being determined at sufficiently high resolution to detect uncharacterized, small subunits. In this work we offer a guide for the mass spectrometric characterization of solvent extraction-based purifications of small membrane proteins isolated from protein complexes and cellular membranes. We first demonstrate our Top-Down MALDI-MS/MS approach on a Photosystem II preparation, analyzing target protein masses between 2.5 and 9 kDa with high accuracy and sensitivity. Then we apply our technique to purify and sequence the mycobacterial ATP synthase c subunit, the molecular target of the antibiotic drug bedaquiline. We show that our approach can be used to directly track and pinpoint single amino acid mutations that lead to antibiotic resistance in only 4 h. While not applicable as a high-throughput pipeline, our MALDI-MS/MS and ISD-based approach can identify and provide valuable sequence information on small membrane proteins, which are inaccessible to conventional Bottom-Up techniques. We show that our approach can be used to unambiguously identify single-point mutations leading to antibiotic resistance in mycobacteria.
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Affiliation(s)
- Jakob Meier-Credo
- Proteomics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Proteomics, Max
Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt am Main, Germany
| | - Laura Preiss
- Structural
Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Imke Wüllenweber
- Proteomics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Proteomics, Max
Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt am Main, Germany
| | - Anja Resemann
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Christoph Nordmann
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Jure Zabret
- Department
of Plant Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Detlev Suckau
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Hartmut Michel
- Molecular
Membrane Biology, Max Planck Institute of
Biophysics, Max-von-Laue-Strasse
3, 60438 Frankfurt
am Main, Germany
| | - Marc M. Nowaczyk
- Department
of Plant Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Thomas Meier
- Department
of Life Sciences, Imperial College London, Exhibition Road, SW7 2AZ London, United Kingdom
| | - Julian D. Langer
- Proteomics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Proteomics, Max
Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt am Main, Germany
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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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Tyunina EY, Barannikov VP, Dunaeva VV, Krasnov AV. Enthalpies of Sublimation and Solvation of Alanine-Containing Dipeptides. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s003602442204032x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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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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10
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Birukou I, Zawadzki M, Graser G, Young S. Protein Characterization by MALDI In-Source Decay Mass Spectrometry in Support of Safety Assessments of Genetically Modified Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10358-10370. [PMID: 34428040 DOI: 10.1021/acs.jafc.1c00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The advancement of mass spectrometry provides advantages for transgenic protein characterization in support of safety assessments of genetically modified crops. Here, we describe how matrix-assisted laser desorption ionization in-source decay (ISD) mass spectrometry (MS) in combination with intact mass and bottom-up analyses can be applied to achieve high confidence in the sequences of transgenic proteins expressed in plants and establish the biochemical equivalence of microbially produced protein surrogates. ISD confirmed 40-60 near terminal residues regardless of the protein size, including the improvement of the coverage of cysteine-rich proteins by the reduction/alkylation of disulfide bonds. Negative ISD significantly improved spectral quality and sequence coverage of acidic proteins. Various post-translational modifications, such as terminal truncations and N-terminal methionine excision and acetylation, were identified in plant-produced proteins by top-down MS. Finally, we demonstrated that a combination of top-down and bottom-up analyses provides high confidence in sequence equivalence of plant and microbially produced proteins.
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Affiliation(s)
- Ivan Birukou
- Syngenta Crop Protection, LLC, P.O. Box 12257, 9 Davis Drive, Durham, North Carolina 27709, United States
| | - Michal Zawadzki
- Jealott's Hill International Research Centre, Syngenta Ltd., Bracknell, Berkshire RG42 6EY, U.K
| | - Gerson Graser
- Syngenta Crop Protection, LLC, P.O. Box 12257, 9 Davis Drive, Durham, North Carolina 27709, United States
| | - Scott Young
- Syngenta Crop Protection, LLC, P.O. Box 12257, 9 Davis Drive, Durham, North Carolina 27709, United States
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11
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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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12
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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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13
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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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14
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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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15
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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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16
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Applications of Matrix-Assisted Laser Desorption Ionization In-Source Decay Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:45-54. [DOI: 10.1007/978-3-030-15950-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Fukuyama Y, Izumi S, Tanaka K. 3-Hydroxy-2-Nitrobenzoic Acid as a MALDI Matrix for In-Source Decay and Evaluation of the Isomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2227-2236. [PMID: 30062476 DOI: 10.1007/s13361-018-2030-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
In in-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry (MS), 1,5-diaminonaphthalene (1,5-DAN) is a most frequently used matrix probably due to the highly sensitive detection of fragment ions. 1,5-DAN is a reducing matrix generating c- and z-series ions by N-Cα bond cleavage. However, it is difficult for reducing matrices to distinguish leucine and isoleucine, and generate c(n-1)-series ions owing to proline (Pro) at residues n. Oxidizing matrices providing a- and x-series ions accompanied by d-series ions by Cα-C bond cleavage solve the problem, but their sensitivity of the ISD fragment ions has been lower than reducing matrices such as 1,5-DAN. Recently, 3-hydroxy-4-nitrobenzoic acid (3H4NBA) had been reported as an oxidizing matrix generating a-series ions with higher intensity compared with conventional oxidizing matrices such as 5-nitrosalicylic acid, but a little lower intensity compared with 1,5-DAN (Anal Chem 88, 8058-8063, 2016). In this study, 3H4NBA isomers (2H3NBA, 2H4NBA, 2H5NBA, 2H6NBA, 3H2NBA, 3H5NBA, 4H2NBA, 4H3NBA, 5H2NBA, and 3H4NBA) were evaluated. All the isomers generated a-series ions accompanied by d-series ions, wherein 3H2NBA, 3H5NBA, 4H2NBA, 4H3NBA, and 5H2NBA were first confirmed as oxidizing matrices for ISD. Among the isomers, 3H2NBA and 4H3NBA generated a-series ions with higher peak intensity compared with 3H4NBA for several peptides. Especially, 3H2NBA generated a-series ions with almost the same or higher intensity, and clearly higher peak resolution compared with c-series ions using 1,5-DAN in several cases. 3H2NBA was expected to contribute to ISD analyses in MALDI-MS as one of the most effective oxidizing matrices. Graphical Abstract ᅟ.
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Affiliation(s)
- Yuko Fukuyama
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1, Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan.
| | - Shunsuke Izumi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1, Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
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18
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Ge YH, Chen YY, Zhou GS, Liu X, Tang YP, Liu R, Liu P, Li N, Yang J, Wang J, Yue SJ, Zhou H, Duan JA. A Novel Antithrombotic Protease from Marine Worm Sipunculus Nudus. Int J Mol Sci 2018; 19:ijms19103023. [PMID: 30287737 PMCID: PMC6213608 DOI: 10.3390/ijms19103023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/23/2018] [Accepted: 09/28/2018] [Indexed: 12/15/2022] Open
Abstract
Sipunculus nudus, an old marine species, has great potential for use as functional seafood due to its various bioactivities. Its potential antithrombotic activity pushed us to isolate the bio-active components bio-guided by tracking fibrinolytic activity. As a result, a novel protease named as SK (the kinase obtained from S. nudus) was obtained, which possessed a molecular weight of 28,003.67 Da and 15 N-terminal amino acid sequences of PFPVPDPFVWDTSFQ. SK exerted inhibitory effects on thrombus formation through improving the coagulation system with dose-effect relationship within a certain range. Furthermore, in most cases SK got obviously better effect than that of urokinase. With the help of untargeted mass spectrometry-based metabolomics profiling, arachidonic acid, sphingolipid, and nicotinate and nicotinamide mechanism pathways were found to be important pathways. They revealed that the effect mechanism of SK on common carotid arterial thrombosis induced by FeCl3 was achieved by inhibiting vessel contraction, platelet aggregation, adhesion, and release, correcting endothelial cell dysfunction and retarding process of thrombus formation. This study demonstrated SK was a promising thrombolytic agent on the basis of its comprehensive activities on thrombosis, and it should get further exploitation and utilization.
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Affiliation(s)
- Ya-Hui Ge
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an 712046, China.
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Yan-Yan Chen
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an 712046, China.
| | - Gui-Sheng Zhou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Xin Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Yu-Ping Tang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an 712046, China.
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Rui Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Pei Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau, China.
| | - Jie Yang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an 712046, China.
| | - Jing Wang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an 712046, China.
| | - Shi-Jun Yue
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an 712046, China.
| | - Huiping Zhou
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA.
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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19
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Resemann A, Liu-Shin L, Tremintin G, Malhotra A, Fung A, Wang F, Ratnaswamy G, Suckau D. Rapid, automated characterization of disulfide bond scrambling and IgG2 isoform determination. MAbs 2018; 10:1200-1213. [PMID: 30277844 PMCID: PMC6284591 DOI: 10.1080/19420862.2018.1512328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human antibodies of the IgG2 subclass exhibit complex inter-chain disulfide bonding patterns that result in three structures, namely A, A/B, and B. In therapeutic applications, the distribution of disulfide isoforms is a critical product quality attribute because each configuration affects higher order structure, stability, isoelectric point, and antigen binding. The current standard for quantification of IgG2 disulfide isoform distribution is based on chromatographic or electrophoretic techniques that require additional characterization using mass spectrometry (MS)-based methods to confirm disulfide linkages. Detailed characterization of the IgG2 disulfide linkages often involve MS/MS approaches that include electrospray ionization or electron-transfer dissociation, and method optimization is often cumbersome due to the large size and heterogeneity of the disulfide-bonded peptides. As reported here, we developed a rapid LC-MALDI-TOF/TOF workflow that can both identify the IgG2 disulfide linkages and provide a semi-quantitative assessment of the distribution of the disulfide isoforms. We established signature disulfide-bonded IgG2 hinge peptides that correspond to the A, A/B, and B disulfide isoforms and can be applied to the fast classification of IgG2 isoforms in heterogeneous mixtures.
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Affiliation(s)
- Anja Resemann
- a BioPharma Solutions R&D , BALS, Bruker Daltonik , Bremen , Germany
| | - Lily Liu-Shin
- b Analytical and Formulation Development, Agensys, Inc., an affiliate of Astellas , Santa Monica , CA , USA.,c Department of Biochemistry and Molecular Biology , University of Miami Miller School of Medicine , Miami , FL , USA
| | | | - Arun Malhotra
- c Department of Biochemistry and Molecular Biology , University of Miami Miller School of Medicine , Miami , FL , USA
| | - Adam Fung
- b Analytical and Formulation Development, Agensys, Inc., an affiliate of Astellas , Santa Monica , CA , USA
| | - Fang Wang
- b Analytical and Formulation Development, Agensys, Inc., an affiliate of Astellas , Santa Monica , CA , USA
| | - Gayathri Ratnaswamy
- b Analytical and Formulation Development, Agensys, Inc., an affiliate of Astellas , Santa Monica , CA , USA
| | - Detlev Suckau
- a BioPharma Solutions R&D , BALS, Bruker Daltonik , Bremen , Germany
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20
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Massonnet P, Haler JRN, Upert G, Smargiasso N, Mourier G, Gilles N, Quinton L, De Pauw E. Disulfide Connectivity Analysis of Peptides Bearing Two Intramolecular Disulfide Bonds Using MALDI In-Source Decay. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1995-2002. [PMID: 29987664 DOI: 10.1007/s13361-018-2022-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/07/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Disulfide connectivity in peptides bearing at least two intramolecular disulfide bonds is highly important for the structure and the biological activity of the peptides. In that context, analytical strategies allowing a characterization of the cysteine pairing are of prime interest for chemists, biochemists, and biologists. For that purpose, this study evaluates the potential of MALDI in-source decay (ISD) for characterizing cysteine pairs through the systematic analysis of identical peptides bearing two disulfide bonds, but not the same cysteine connectivity. Three different matrices have been tested in positive and/or in negative mode (1,5-DAN, 2-AB and 2-AA). As MALDI-ISD is known to partially reduce disulfide bonds, the data analysis of this study rests firstly on the deconvolution of the isotope pattern of the parent ions. Moreover, data analysis is also based on the formed fragment ions and their signal intensities. Results from MS/MS-experiments (MALDI-ISD-MS/MS) constitute the last reference for data interpretation. Owing to the combined use of different ISD-promoting matrices, cysteine connectivity identification could be performed on the considered peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Philippe Massonnet
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium.
| | - Jean R N Haler
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Gregory Upert
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Gilles Mourier
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Nicolas Gilles
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
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21
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Tibery DV, Campos LA, Mourão CBF, Peigneur S, E Carvalho AC, Tytgat J, Schwartz EF. Electrophysiological characterization of Tityus obscurus β toxin 1 (To1) on Na +-channel isoforms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:142-150. [PMID: 30463697 DOI: 10.1016/j.bbamem.2018.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Abstract
To1, previously named Tc49b, is a peptide neurotoxin isolated from venom of the scorpion Tityus obscurus that is responsible for lethal human poisoning cases in the Brazilian Amazonian region. Previously, To1 was shown to be lethal to mice and to change Na+ permeation in cerebellum granular neurons from rat brain. In addition, To1 did not affect Shaker B K+ channels. Based on sequence similarities, To1 was described as a β-toxin. In the present work, To1 was purified from T. obscurus venom and submitted to an electrophysiological characterization in human and invertebrate NaV channels. The analysis of the electrophysiological experiments reveal that To1 enhances the open probability at more negative potentials of human NaV 1.3 and 1.6, of the insect channel BgNaV1 and of arachnid VdNaV1 channel. In addition, To1 reduces the peak of Na+ currents in some of the NaVs tested. These results support the classification of the To1 as a β-toxin. A structure and functional comparison to other β-toxins that share sequence similarity to To1 is also presented.
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Affiliation(s)
- Diogo Vieira Tibery
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Leandro Ambrósio Campos
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Caroline Barbosa Farias Mourão
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de Brasília, Campus Ceilândia, Brasília, Distrito Federal, Brazil
| | - Steve Peigneur
- Toxicology and Pharmacology, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven (KU Leuven), Leuven, Belgium
| | - Andréa Cruz E Carvalho
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Jan Tytgat
- Toxicology and Pharmacology, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven (KU Leuven), Leuven, Belgium
| | - Elisabeth Ferroni Schwartz
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil.
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22
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Glycine Oligomerization by Pulsed Discharge Plasma over Aqueous Solution under Atmospheric Pressure. CHEMENGINEERING 2018. [DOI: 10.3390/chemengineering2020017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Asakawa D, Takahashi H, Iwamoto S, Tanaka K. Fundamental study of hydrogen-attachment-induced peptide fragmentation occurring in the gas phase and during the matrix-assisted laser desorption/ionization process. Phys Chem Chem Phys 2018; 20:13057-13067. [DOI: 10.1039/c8cp00733k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mass spectrometry with hydrogen-radical-mediated fragmentation techniques has been used for the sequencing of proteins/peptides.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST)
- Ibaraki
- Japan
| | - Hidenori Takahashi
- Koichi Tanaka Mass Spectrometry Research Laboratory
- Shimadzu Corporation
- Kyoto 604-8511
- Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory
- Shimadzu Corporation
- Kyoto 604-8511
- Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory
- Shimadzu Corporation
- Kyoto 604-8511
- Japan
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24
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Covaleda G, Trejo SA, Salas-Sarduy E, Del Rivero MA, Chavez MA, Aviles FX. Intensity fading MALDI-TOF mass spectrometry and functional proteomics assignments to identify protease inhibitors in marine invertebrates. J Proteomics 2017; 165:75-92. [PMID: 28602552 DOI: 10.1016/j.jprot.2017.05.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/20/2017] [Accepted: 05/31/2017] [Indexed: 12/14/2022]
Abstract
Proteases and their inhibitors have become molecules of increasing fundamental and applicative value. Here we report an integrated strategy to identify and analyze such inhibitors from Caribbean marine invertebrates extracts by a fast and sensitive functional proteomics-like approach. The strategy works in three steps: i) multiplexed enzymatic inhibition kinetic assays, ii) Intensity Fading MALDI-TOF MS to establish a link between inhibitory molecules and the related MALDI signal(s) detected in the extract(s), and iii) ISD-CID-T3 MS fragmentation on the parent MALDI signals selected in the previous step, enabling the partial or total top-down sequencing of the molecules. The present study has allowed validation of the whole approach, identification of a substantial number of novel protein protease inhibitors, as well as full or partial sequencing of reference molecular species and of many unknown ones, respectively. Such inhibitors correspond to six protease subfamilies (metallocarboxypeptidases-A and -B, pepsin, papain, trypsin and subtilisin), are small (1-10KDa) disulfide-rich proteins, and have been found at diverse frequencies among the invertebrates (13 to 41%). The overall procedure could be tailored to other enzyme-inhibitor and protein interacting systems, analyzing samples at medium-throughput level and leading to the functional and structural characterization of proteinaceous ligands from complex biological extracts. SIGNIFICANCE Invertebrate animals, and marine ones among, display a remarkable diversity of species and contained biomolecules. Many of their proteins-peptides have high biological, biotechnological and biomedical potential interest but, because of the lack of sequenced genomes behind, their structural and functional characterization constitutes a great challenge. Here, looking at the small, disulfide-rich, proteinaceous inhibitors of proteases found in them, it is shown that such problem can be significatively facilitated by integrative multiplexed enzymatic assays, affinity-based Intensity-Fading (IF-) MALDI-TOF mass spectrometry (MS), and on-line MS fragmentation, in a fast and easy approach.
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Affiliation(s)
- Giovanni Covaleda
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Sebastian A Trejo
- Servei de Proteomica i Biologia Estructural SePBioEs, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Emir Salas-Sarduy
- Centro de Estudio de Proteinas, Facultad de Biologia, Universidad de la Habana, Cuba
| | | | - Maria Angeles Chavez
- Centro de Estudio de Proteinas, Facultad de Biologia, Universidad de la Habana, Cuba.
| | - Francesc X Aviles
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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25
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Organic matrices, ionic liquids, and organic matrices@nanoparticles assisted laser desorption/ionization mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.01.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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Calvano CD, Ventura G, Trotta M, Bianco G, Cataldi TRI, Palmisano F. Electron-Transfer Secondary Reaction Matrices for MALDI MS Analysis of Bacteriochlorophyll a in Rhodobacter sphaeroides and Its Zinc and Copper Analogue Pigments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:125-135. [PMID: 27730524 DOI: 10.1007/s13361-016-1514-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 09/05/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
Bacteriochlorophyll a (BChl a), a photosynthetic pigment performing the same functions of chlorophylls in plants, features a bacteriochlorin macrocycle ring (18 π electrons) with two reduced pyrrole rings along with a hydrophobic terpenoid side chain (i.e., the phytol residue). Chlorophylls analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is not so straightforward since pheophytinization (i.e., release of the central metal ion) and cleavage of the phytol-ester linkage are invariably observed by employing protonating matrices such as 2,5-dihydroxybenzoic acid, sinapinic acid, and α-cyano-4-hydroxycinnamic acid. Using BChl a from Rhodobacter sphaeroides R26 strain as a model system, different electron-transfer (ET) secondary reaction matrices, leading to the formation of almost stable radical ions in both positive ([M]+•) and negative ([M]-•) ionization modes at m/z 910.55, were evaluated. Compared with ET matrices such as trans-2-[3-(4-t-butyl-phenyl)-2-methyl-2-propenylidene]malononitrile (DCTB), 2,2':5',2''-terthiophene (TER), anthracene (ANT), and 9,10-diphenylanthracene (DP-ANT), 1,5-diaminonaphthalene (DAN) was found to provide the highest ionization yield with a negligible fragmentation. DAN also displayed excellent ionization properties for two metal ion-substituted bacteriochlorophylls, (i.e., Zn- and Cu-BChl a at m/z 950.49 and 949.49), respectively. MALDI MS/MS of both radical charged molecular species provide complementary information, thus making analyte identification more straightforward. Graphical Abstract ᅟ.
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Affiliation(s)
- Cosima Damiana Calvano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Campus Universitario, Via E. Orabona, 4, 70126, Bari, Italy
- Centro di Ricerca Interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Campus Universitario, Via E. Orabona, 4, 70126, Bari, Italy
| | - Giovanni Ventura
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Campus Universitario, Via E. Orabona, 4, 70126, Bari, Italy
| | - Massimo Trotta
- Istituto Processi Chimico Fisici CNR, Università degli Studi di Bari Aldo Moro, Campus Universitario, Via E. Orabona, 4, 70126, Bari, Italy
| | - Giuliana Bianco
- Dipartimento di Scienze, Università degli Studi della Basilicata, Via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Tommaso R I Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Campus Universitario, Via E. Orabona, 4, 70126, Bari, Italy.
- Centro di Ricerca Interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Campus Universitario, Via E. Orabona, 4, 70126, Bari, Italy.
| | - Francesco Palmisano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Campus Universitario, Via E. Orabona, 4, 70126, Bari, Italy
- Centro di Ricerca Interdipartimentale SMART, Università degli Studi di Bari Aldo Moro, Campus Universitario, Via E. Orabona, 4, 70126, Bari, Italy
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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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Fukuyama Y, Izumi S, Tanaka K. 3-Hydroxy-4-nitrobenzoic Acid as a MALDI Matrix for In-Source Decay. Anal Chem 2016; 88:8058-63. [PMID: 27467192 DOI: 10.1021/acs.analchem.6b01471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) is a rapid sequencing method for peptides. 1,5-Diaminonaphthalene (1,5-DAN) is a most frequently used matrix for ISD. However, using 1,5-DAN generates mainly c- and z-series ions by N-Cα bond cleavage, which makes it difficult to distinguish leucine (Leu) and isoleucine (Ile), and frequently lacks c(n-1)-series ions owing to proline (Pro) at residues n. Several oxidizing matrices generating a- and x-series ions accompanied by d-series ions by Cα-C bond cleavage have been reported, but an issue remained concerning their sensitivity. 3-Hydroxy-4-nitrobenzoic acid (3H4NBA) has been reported as a matrix for 2-nitrobenzenesulfenyl-labeled peptides by Matsuo et al. (Proteomics 2006, 6, 2042-2049). Here, we used 3H4NBA as an oxidizing matrix for ISD. As a result, numerous a- and d-series ions for amyloid β 1-40 were generated with high sensitivity using 3H4NBA. Each of the two Leu and two Ile was identified by the d-series ions. The sensitivity of the a-series ions using 3H4NBA was a little lower than that of c-series ions using 1,5-DAN. The same tendency was observed for N-acetyl renin substrate and ACTH 18-39. The a-series ions were detected, even at the left side of Pro. The sensitivity of the a-series ions using 3H4NBA was higher than with other existing oxidizing matrices, such as 5-nitrosalicylic acid and 5-formyl salycilic acid. The ions were detected over the entire area of the matrix-analyte spot using 3H4NBA. 3H4NBA was confirmed to be a useful oxidizing matrix for ISD, leading to higher sequence coverage of peptides.
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Affiliation(s)
- Yuko Fukuyama
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation , 1, Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shunsuke Izumi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation , 1, Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
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29
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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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30
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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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31
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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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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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Resemann A, Jabs W, Wiechmann A, Wagner E, Colas O, Evers W, Belau E, Vorwerg L, Evans C, Beck A, Suckau D. Full validation of therapeutic antibody sequences by middle-up mass measurements and middle-down protein sequencing. MAbs 2016; 8:318-30. [PMID: 26760197 PMCID: PMC4966597 DOI: 10.1080/19420862.2015.1128607] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The regulatory bodies request full sequence data assessment both for innovator and biosimilar monoclonal antibodies (mAbs). Full sequence coverage is typically used to verify the integrity of the analytical data obtained following the combination of multiple LC-MS/MS datasets from orthogonal protease digests (so called “bottom-up” approaches). Top-down or middle-down mass spectrometric approaches have the potential to minimize artifacts, reduce overall analysis time and provide orthogonality to this traditional approach. In this work we report a new combined approach involving middle-up LC-QTOF and middle-down LC-MALDI in-source decay (ISD) mass spectrometry. This was applied to cetuximab, panitumumab and natalizumab, selected as representative US Food and Drug Administration- and European Medicines Agency-approved mAbs. The goal was to unambiguously confirm their reference sequences and examine the general applicability of this approach. Furthermore, a new measure for assessing the integrity and validity of results from middle-down approaches is introduced – the “Sequence Validation Percentage.” Full sequence data assessment of the 3 antibodies was achieved enabling all 3 sequences to be fully validated by a combination of middle-up molecular weight determination and middle-down protein sequencing. Three errors in the reference amino acid sequence of natalizumab, causing a cumulative mass shift of only −2 Da in the natalizumab Fd domain, were corrected as a result of this work.
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Affiliation(s)
- Anja Resemann
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Wolfgang Jabs
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Anja Wiechmann
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Elsa Wagner
- b Centre d'Immunologie Pierre , St Julien-en-Genevois, France
| | - Olivier Colas
- b Centre d'Immunologie Pierre , St Julien-en-Genevois, France
| | - Waltraud Evers
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Eckhard Belau
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Lars Vorwerg
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | | | - Alain Beck
- b Centre d'Immunologie Pierre , St Julien-en-Genevois, France
| | - Detlev Suckau
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
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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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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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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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Improvement of chlorophyll identification in foodstuffs by MALDI ToF/ToF mass spectrometry using 1,5-diaminonaphthalene electron transfer secondary reaction matrix. Anal Bioanal Chem 2015; 407:6369-79. [PMID: 25976392 DOI: 10.1007/s00216-015-8728-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/16/2015] [Accepted: 04/20/2015] [Indexed: 10/23/2022]
Abstract
Chlorophylls (Chls) are important pigments responsible for the characteristic green color of chloroplasts in algae and plants. In this study, 1,5-diaminonaphthalene (DAN) was introduced as an electron transfer secondary reaction matrix for the identification of intact chlorophylls and their derivatives, by matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS). DAN was proved to drastically outperform conventional matrices such as α-cyano-4-hydroxycinnnamic acid, dithranol, antracene, and even terthiophene, since loss of the metal ion and fragmentation of the phytol-ester linkage are negligible. Absence of significant fragmentation of radical cations of Chls a and b at m/z 892.529 and 906.513, respectively, makes MALDI MS capable of following natural degradation of intact porphyrin-based pigments whose initial steps are just represented by demetalation and dephytylation. Chl by-products, such as pyropheophytins, have been identified in dried tea leaves showing the potential of MALDI MS to follow chlorophyll biotransformation occurring in processed foodstuffs. Finally, preliminary results show the potential of MALDI MS to detect illegal vegetable oil re-greening practices.
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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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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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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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Liang Q, Macher T, Xu Y, Bao Y, Cassady CJ. MALDI MS In-Source Decay of Glycans Using a Glutathione-Capped Iron Oxide Nanoparticle Matrix. Anal Chem 2014; 86:8496-503. [DOI: 10.1021/ac502422a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Qiaoli Liang
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Thomas Macher
- Department
of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Yaolin Xu
- Department
of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Yuping Bao
- Department
of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carolyn J. Cassady
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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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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46
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Ait-Belkacem R, Berenguer C, Villard C, Ouafik L, Figarella-Branger D, Chinot O, Lafitte D. MALDI imaging and in-source decay for top-down characterization of glioblastoma. Proteomics 2014; 14:1290-301. [PMID: 24376047 DOI: 10.1002/pmic.201300329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/27/2013] [Accepted: 10/04/2013] [Indexed: 01/15/2023]
Abstract
Glioblastoma multiforme is one of the most common intracranial tumors encountered in adults. This tumor of very poor prognosis is associated with a median survival rate of approximately 14 months. One of the major issues to better understand the biology of these tumors and to optimize the therapy is to obtain the molecular structure of glioblastoma. MALDI molecular imaging enables location of molecules in tissues without labeling. However, molecular identification in situ is not an easy task. In this paper, we used MALDI imaging coupled to in-source decay to characterize markers of this pathology. We provided MALDI molecular images up to 30 μm spatial resolution of mouse brain tissue sections. MALDI images showed the heterogeneity of the glioblastoma. In the various zones and at various development stages of the tumor, using our top-down strategy, we identified several proteins. These proteins play key roles in tumorigenesis. Particular attention was given to the necrotic area with characterization of hemorrhage, one of the most important poor prognosis factors in glioblastoma.
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Iimuro R, Takayama M. Analysis of Flexibility of Proteins by means of Positive and Negative Ion MALDI In-Source Decay Mass Spectrometry. Mass Spectrom (Tokyo) 2014; 3:S0023. [PMID: 26819895 PMCID: PMC4622517 DOI: 10.5702/massspectrometry.s0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/19/2013] [Indexed: 02/03/2023] Open
Abstract
The amino acid residues susceptible to in-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry have been identified from both positive and negative ion ISD spectra of cytochrome c, myoglobin, thioredoxin and bovine serum albumin. Backbone cleavages at the N-Cα bonds of Xxx-Asp, Xxx-Asn, Xxx-Cys, and Gly-Xxx residues gave discontinuous intense peaks of c-ions, independent of positive and negative ion mode. The intensity values for c-ions, Int(c), were defined to allow estimation of the discontinuous intense peaks of c-ions. The identities of the high intensity value residues Asp, Asn, Cys, and Gly were compared with those identified using other measures of flexibility such as the B-factor, turn preferential factor and protection factor. The comparison indicates that Asp, Asn, and Gly residues are common to all measures. Thus, the intensity values of c-ions can be adopted as a measure of protein flexibility.
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Affiliation(s)
- Ryunosuke Iimuro
- Graduate School of Nanobioscience, Mass Spectrometry Laboratory, Yokohama City University
| | - Mitsuo Takayama
- Graduate School of Nanobioscience, Mass Spectrometry Laboratory, Yokohama City University
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Takayama M, Sekiya S, Iimuro R, Iwamoto S, Tanaka K. Selective and nonselective cleavages in positive and negative CID of the fragments generated from in-source decay of intact proteins in MALDI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:120-131. [PMID: 24135807 DOI: 10.1007/s13361-013-0756-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/13/2013] [Accepted: 09/16/2013] [Indexed: 06/02/2023]
Abstract
Selective and nonselective cleavages in ion trap low-energy collision-induced dissociation (CID) experiments of the fragments generated from in-source decay (ISD) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) of intact proteins are described in both positive and negative ion modes. The MALDI-ISD spectra of the proteins demonstrate common, discontinuous, abundant c- and z'-ions originating from cleavage at the N-Cα bond of Xxx-Asp/Asn and Gly-Xxx residues in both positive- and negative-ion modes. The positive ion CID of the c- and z'-ions resulted in product ions originating from selective cleavage at Asp-Xxx, Glu-Xxx and Cys-Xxx residues. Nonselective cleavage product ions rationalized by the mechanism of a "mobile proton" are also observed in positive ion CID spectra. Negative ion CID of the ISD fragments results in complex product ions accompanied by the loss of neutrals from b-, c-, and y-ions. The most characteristic feature of negative ion CID is selective cleavage of the peptide bonds of acidic residues, Xxx-Asp/Glu/Cys. A definite influence of α-helix on the CID product ions was not obtained. However, the results from positive ion and negative ion CID of the MALDI-ISD fragments that may have long α-helical domains suggest that acidic residues in helix-free regions tend to degrade more than those in helical regions.
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Affiliation(s)
- Mitsuo Takayama
- Graduate School in Nanobioscience, Mass Spectrometry Laboratory, Yokohama City University, Kanazawa-ku, Yokohama, Japan,
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Lemaire P, Debois D, Smargiasso N, Quinton L, Gabelica V, De Pauw EA. Use of 1,5-diaminonaphthalene to combine matrix-assisted laser desorption/ionization in-source decay fragmentation with hydrogen/deuterium exchange. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1837-1846. [PMID: 23857929 DOI: 10.1002/rcm.6627] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE In-Source Decay (ISD) in Matrix-Assisted Laser Desorption/Ionization (MALDI) mass spectrometry is a fast and easy top-down activation method. Our objective is to find a suitable matrix to locate the deuterons following in-solution hydrogen/deuterium exchange (HDX). This matrix must circumvent the commonly encountered undesired back-exchange reactions, in order to preserve the regioselective deuteration pattern. METHODS The 1,5-diaminonaphthalene (1,5-DAN) matrix is known to be suitable for MALDI-ISD fragmentation. MALDI Mass Spectrometry Imaging (MSI) was employed to compare 1,5-DAN and other commonly used MALDI matrices with respect to the extent of back-exchange and the uniformity of the H/D exchange profiles within the MALDI spots. We tested the back-exchange on the highly sensitive amyloid-beta peptide (1-40), and proved the regioselectivity on ubiquitin and β-endorphin. RESULTS MALDI-MSI results show that 1,5-DAN leads to the least back-exchange over all the spot. MALDI-ISD fragmentation combined with H/D exchange using 1,5-DAN matrix was validated by localizing deuterons in native ubiquitin. Results agree with previous data obtained by Nuclear Magnetic Resonance (NMR) and Electron Transfer Dissociation (ETD). Moreover, 1,5-DAN matrix was used to study the H/D exchange profile of the methanol-induced helical structure of β-endorphin, and the relative protection can be explained by the polarity of residues involved in hydrogen bond formation. CONCLUSIONS We found that controlling crystallization is the most important parameter when combining H/D exchange with MALDI. The 1,5-DAN matrix is characterized by a fast crystallization kinetics, and therefore gives robust and reliable H/D exchange profiles using MALDI-ISD.
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Affiliation(s)
- Pascale Lemaire
- GIGA-R, Mass Spectrometry Laboratory, Department of Chemistry, Chemistry Building B6c, University of Liège, B-4000 Liège, Belgium
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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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