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Klapper FA, Kiel C, Bellstedt P, Vyverman W, Pohnert G. Structure Elucidation of the First Sex-Inducing Pheromone of a Diatom. Angew Chem Int Ed Engl 2023; 62:e202307165. [PMID: 37607131 DOI: 10.1002/anie.202307165] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
Diatoms are abundant unicellular microalgae, responsible for ≈20 % of global photosynthetic CO2 fixation. Nevertheless, we know little about fundamental aspects of their biology, such as their sexual reproduction. Pheromone-mediated chemical communication is crucial for successful mating. An attraction pheromone was identified in the diatom Seminavis robusta, but metabolites priming cells for sex and synchronizing search and mating behavior remained elusive. These sex-inducing pheromones (SIP) induce cell cycle arrest and trigger the production of the attraction pheromone. Here we describe the challenging structure elucidation of an S. robusta SIP. Guided by metabolomics, a candidate metabolite was identified and elucidated by labeling experiments, NMR, ESI MSn analyses, and chemical transformations. The use of negative ion mode MS was essential to decipher the unprecedented hydroxyproline and β-sulfated aspartate-containing cyclic heptapeptide that acts in femtomolar concentrations.
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Affiliation(s)
- Franziska A Klapper
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstrasse 8, 07743, Jena, Germany
| | - Christine Kiel
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstrasse 8, 07743, Jena, Germany
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Zur alten Fischerhütte 2, 16775, Stechlin, Germany
| | - Peter Bellstedt
- Institute of Organic and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
- Institute of Clinical Chemistry, University of Zurich & University Hospital, Rämistrasse 100, 8091, Zürich, Switzerland
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281 S8, 9000, Ghent, Belgium
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstrasse 8, 07743, Jena, Germany
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany
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2
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Tolpina MD, Vasileva ID, Samgina TY. Modern Approaches in de novo Sequencing of Nontryptic Peptides of Ranid and Hylid Frogs by Means of Mass Spectrometry: A Review. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822130081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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3
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Lebedev AT, Vasileva ID, Samgina TY. FT-MS in the de novo top-down sequencing of natural nontryptic peptides. MASS SPECTROMETRY REVIEWS 2022; 41:284-313. [PMID: 33347655 DOI: 10.1002/mas.21678] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
The present review covers available results on the application of FT-MS for the de novo sequencing of natural peptides of various animals: cones, bees, snakes, amphibians, scorpions, and so forth. As these peptides are usually bioactive, the animals efficiently use them as a weapon against microorganisms or higher animals including predators. These peptides represent definite interest as drugs of future generations since the mechanism of their activity is completely different in comparison with that of the modern antibiotics. Utilization of those peptides as antibiotics can eliminate the problem of the bacterial resistance development. Sequence elucidation of these bioactive peptides becomes even more challenging when the species genome is not available and little is known about the protein origin and other properties of those peptides in the study. De novo sequencing may be the only option to obtain sequence information. The benefits of FT-MS for the top-down peptide sequencing, the general approaches of the de novxxo sequencing, the difficult cases involving sequence coverage, isobaric and isomeric amino acids, cyclization of short peptides, the presence of posttranslational modifications will be discussed in the review.
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Affiliation(s)
- Albert T Lebedev
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Irina D Vasileva
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Y Samgina
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
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4
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Guan S, Rabus JM, Maître P, Bythell BJ. Gas-Phase Dissociation Chemistry of Deprotonated RGD. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:55-63. [PMID: 32267154 DOI: 10.1021/jasms.0c00074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We investigate the structure and dissociation pathways of the deprotonated amphoteric peptide arginylglycylasparic acid, [RGD-H]-. We model the pertinent gas-phase structures and fragmentation chemistry of the precursor anions and predominant sequence-informative bond cleavages (b2+H2O, c2, and z1 peaks) and compare these predictions to our tandem mass spectra and infrared spectroscopy experiments. Formation of the b2+H2O anions requires rate-limiting intramolecular back biting to cleave the second amide bond and generate an anhydride structure. Facile cleavage of the newly formed ester bond with concerted expulsion of a cyclic anhydride neutral generates the product structure. IR spectroscopy supports this b2+H2O anion having structures that are essentially identical to C-terminally deprotonated arginylglycine, [RG-H]-. Formation of the c2 anion is predicted to require concerted expulsion of CO2 from the aspartyl side chain carboxylate and cleavage of the N-Calpha bond to produce a proton-bound dimer of arginylglycinamide and acrylate. Proton transfers within the dimer then enable predominant detection of a c2 anion with the negative charge nominally on the central, glycine nitrogen (amidate structure) as the proton affinity of this structure is predicted to be lower than acrylate by ∼27 kJ mol-1. Alternate means of cleaving the same N-Calpha bond produce deprotonated cis-1,4-dibut-2-enoic acid z1 anion structures. These lowest energy processes involve C-H proton mobilization from the aspartyl side chain prior to N-Calpha bond cleavage consistent with proposals from the literature.
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Affiliation(s)
- Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Philippe Maître
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
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5
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Malik A, Lin YF, Pratihar S, Angel LA, Hase WL. Direct Dynamics Simulations of Fragmentation of a Zn(II)-2Cys-2His Oligopeptide. Comparison with Mass Spectrometry Collision-Induced Dissociation. J Phys Chem A 2019; 123:6868-6885. [DOI: 10.1021/acs.jpca.9b05218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Abdul Malik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
| | - Yu-Fu Lin
- Department of Chemistry Texas A&M University—Commerce, 2600 South Neal Street, Commerce, Texas 75428, United States
| | - Subha Pratihar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
| | - Laurence A. Angel
- Department of Chemistry Texas A&M University—Commerce, 2600 South Neal Street, Commerce, Texas 75428, United States
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
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6
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Katsanovskaja K, Driver T, Pipkorn R, Edelson-Averbukh M. Negative Ion Mode Collision-Induced Dissociation for Analysis of Protein Arginine Methylation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1229-1241. [PMID: 30915654 PMCID: PMC6591203 DOI: 10.1007/s13361-019-02176-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 02/21/2019] [Accepted: 03/01/2019] [Indexed: 06/09/2023]
Abstract
Arginine methylation is a common protein post-translational modification (PTM) that plays a key role in eukaryotic cells. Three distinct types of this modification are found in mammals: asymmetric Nη1Nη1-dimethylarginine (aDMA), symmetric Nη1Nη2-dimethylarginine (sDMA), and an intermediate Nη1-monomethylarginine (MMA). Elucidation of regulatory mechanisms of arginine methylation in living organisms requires precise information on both the type of the modified residues and their location inside the protein amino acid sequences. Despite mass spectrometry (MS) being the method of choice for analysis of multiple protein PTMs, unambiguous characterization of protein arginine methylation may not be always straightforward. Indeed, frequent internal basic residues of Arg methylated tryptic peptides hamper their sequencing under positive ion mode collision-induced dissociation (CID), the standardly used tandem mass spectrometry method, while the relative stability of the aDMA and sDMA side chains under alternative non-ergodic electron-based fragmentation techniques, electron-capture and electron transfer dissociations (ECD and ETD), may impede differentiation between the isobaric residues. Here, for the first time, we demonstrate the potential of the negative ion mode collision-induced dissociation MS for analysis of protein arginine methylation and present data revealing that the negative polarity approach can deliver both an unambiguous identification of the arginine methylation type and extensive information on the modified peptide sequences.
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Affiliation(s)
| | - Taran Driver
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Rüdiger Pipkorn
- Department of Translational Immunology, German Cancer Research Centre, INF 580, 69120, Heidelberg, Germany
| | - Marina Edelson-Averbukh
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK.
- Department of Physics, Imperial College London, London, SW7 2AZ, UK.
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7
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Macaluso V, Scuderi D, Crestoni ME, Fornarini S, Corinti D, Dalloz E, Martinez-Nunez E, Hase WL, Spezia R. l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations. J Phys Chem A 2019; 123:3685-3696. [DOI: 10.1021/acs.jpca.9b01779] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
| | - Debora Scuderi
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Enzo Dalloz
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Emilio Martinez-Nunez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, 4, Place Jussieu, 75252 Paris Cedex 05, France
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8
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Gaillard M, Das S, Djibo M, Raviglione D, Roumestand C, Legrand B, Inguimbert N. Towards the total synthesis of trichormamide A, a cyclic undecapeptide. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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9
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MacAleese L, Girod M, Nahon L, Giuliani A, Antoine R, Dugourd P. Radical Anions of Oxidized vs. Reduced Oxytocin: Influence of Disulfide Bridges on CID and Vacuum UV Photo-Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1826-1834. [PMID: 29949057 DOI: 10.1007/s13361-018-1989-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/27/2018] [Accepted: 05/05/2018] [Indexed: 06/08/2023]
Abstract
The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are fundamental for protein structure, could also be responsible for an increased resistance to ionizing radiations. Graphical Abstract.
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Affiliation(s)
- Luke MacAleese
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France.
| | - Marion Girod
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques UMR 5280, 69100, Villeurbanne, France
| | - Laurent Nahon
- Synchrotron SOLEIL, BP 48 St Aubin, 91192, Gif Sur Yvette, France
| | - Alexandre Giuliani
- Synchrotron SOLEIL, BP 48 St Aubin, 91192, Gif Sur Yvette, France
- UAR1008 CEPIA, INRA, BP 71627, 44316, Nantes, France
| | - Rodolphe Antoine
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France
| | - Philippe Dugourd
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France
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10
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Degradation of cocoa proteins into oligopeptides during spontaneous fermentation of cocoa beans. Food Res Int 2018; 109:506-516. [DOI: 10.1016/j.foodres.2018.04.068] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/27/2018] [Accepted: 04/29/2018] [Indexed: 12/11/2022]
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11
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Liang Y, Neta P, Yang X, Stein SE. Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:463-469. [PMID: 29143271 DOI: 10.1007/s13361-017-1842-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Yuxue Liang
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
| | - Pedatsur Neta
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Xiaoyu Yang
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Stephen E Stein
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
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12
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Martin-Somer A, Martens J, Grzetic J, Hase WL, Oomens J, Spezia R. Unimolecular Fragmentation of Deprotonated Diproline [Pro2-H]− Studied by Chemical Dynamics Simulations and IRMPD Spectroscopy. J Phys Chem A 2018; 122:2612-2625. [DOI: 10.1021/acs.jpca.7b11873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ana Martin-Somer
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, CEA-CNRS, Université Paris Saclay, Evry 91025, France
- Departamento de Química, Facultad de Ciencias, Módulo
13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Josipa Grzetic
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 908, 1098XH Amsterdam, The Netherlands
| | - Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, CEA-CNRS, Université Paris Saclay, Evry 91025, France
- Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F. 75005 Paris, France
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13
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Wang T, Nha Tran TT, Andreazza HJ, Bilusich D, Brinkworth CS, Bowie JH. Negative ion cleavages of (M-H) - anions of peptides. Part 3. Post-translational modifications. MASS SPECTROMETRY REVIEWS 2018; 37:3-21. [PMID: 27018865 DOI: 10.1002/mas.21501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 03/03/2015] [Indexed: 06/05/2023]
Abstract
It is now 25 years since we commenced the study of the negative-ion fragmentations of peptides and we have recently concluded this research with investigations of the negative-ion chemistry of most post-translational functional groups. Our first negative-ion peptide review (Bowie, Brinkworth, & Dua, 2002) dealt with the characteristic backbone fragmentations and side-chain cleavages from (M-H)- ions of underivatized peptides, while the second (Bilusich & Bowie, 2009) included negative-ion backbone cleavages for Ser and Cys and some initial data on some post-translational groups including disulfides. This third and final review provides a brief summary of the major backbone and side chain cleavages outlined before (Bowie, Brinkworth, & Dua, 2002) and describes the quantum mechanical hydrogen tunneling associated with some proton transfers in enolate anion/enolate systems. The review then describes, in more depth, the negative-ion cleavages of the post-translational groups Kyn, isoAsp, pyroglu, disulfides, phosphates, and sulfates. Particular emphasis is devoted to disulfides (both intra- and intermolecular) and phosphates because of the extensive and spectacular anion chemistry shown by these groups. © 2016 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Tianfang Wang
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
- Genecology Research Centre, University of the Sunshine Coast, Queensland, 4556, Australia
| | - T T Nha Tran
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
- Industrial University of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hayley J Andreazza
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
| | - Daniel Bilusich
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
- Defence Science and Technology Organisation, Salisbury, PO Box 1500, South Australia, 5108, Australia
| | - Craig S Brinkworth
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
- Defence Science and Technology Organisation, Land Division, Fishermans Bend, Victoria, 3207, Australia
| | - John H Bowie
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
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14
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Peng Z, Bu J, McLuckey SA. The Generation of Dehydroalanine Residues in Protonated Polypeptides: Ion/Ion Reactions for Introducing Selective Cleavages. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1765-1774. [PMID: 28497355 PMCID: PMC5681889 DOI: 10.1007/s13361-017-1672-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/02/2017] [Accepted: 03/19/2017] [Indexed: 06/07/2023]
Abstract
We examine a gas-phase approach for converting a subset of amino acid residues in polypeptide cations to dehydroalanine (Dha). Subsequent activation of the modified polypeptide ions gives rise to specific cleavage N-terminal to the Dha residue. This process allows for the incorporation of selective cleavages in the structural characterization of polypeptide ions. An ion/ion reaction within the mass spectrometer between a multiply protonated polypeptide and the sulfate radical anion introduces a radical site into the multiply protonated polypeptide reactant. Subsequent collisional activation of the polypeptide radical cation gives rise to radical side chain loss from one of several particular amino acid side chains (e.g., leucine, asparagine, lysine, glutamine, and glutamic acid) to yield a Dha residue. The Dha residues facilitate preferential backbone cleavages to produce signature c- and z-ions, demonstrated with cations derived from melittin, mechano growth factor (MGF), and ubiquitin. The efficiencies for radical side chain loss and for subsequent generation of specific c- and z-ions have been examined as functions of precursor ion charge state and activation conditions using cations of ubiquitin as a model for a small protein. It is noted that these efficiencies are not strongly dependent on ion trap collisional activation conditions but are sensitive to precursor ion charge state. Moderate to low charge states show the greatest overall yields for the specific Dha cleavages, whereas small molecule losses (e.g., water/ammonia) dominate at the lowest charge states and proton catalyzed amide bond cleavages that give rise to b- and y-ions tend to dominate at high charge states. Graphical Abstract ᅟ.
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Affiliation(s)
- Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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15
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Pilo AL, Peng Z, McLuckey SA. The dehydroalanine effect in the fragmentation of ions derived from polypeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:857-866. [PMID: 27484024 PMCID: PMC5068825 DOI: 10.1002/jms.3831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 05/11/2023]
Abstract
The fragmentation of peptides and proteins upon collision-induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non-proteinogenic amino acid with an unsaturated side-chain, undergo enhanced cleavage of the N-Cα bond of the dehydroalanine residue to generate c- and z-ions. Because these fragment ion types are not commonly observed upon activation of positively charged even-electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S-alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas-phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S-alkyl cysteine residues and conversion of multiply-protonated peptides to radical cations. In the latter case, loss of radical side-chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue-specific backbone cleavage of polypeptide ions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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16
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Zheng Q, Chen H. Development and Applications of Liquid Sample Desorption Electrospray Ionization Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:411-448. [PMID: 27145689 DOI: 10.1146/annurev-anchem-071015-041620] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Desorption electrospray ionization mass spectrometry (DESI-MS) is a recent advance in the field of analytical chemistry. This review surveys the development of liquid sample DESI-MS (LS-DESI-MS), a variant form of DESI-MS that focuses on fast analysis of liquid samples, and its novel analy-tical applications in bioanalysis, proteomics, and reaction kinetics. Due to the capability of directly ionizing liquid samples, liquid sample DESI (LS-DESI) has been successfully used to couple MS with various analytical techniques, such as microfluidics, microextraction, electrochemistry, and chromatography. This review also covers these hyphenated techniques. In addition, several closely related ionization methods, including transmission mode DESI, thermally assisted DESI, and continuous flow-extractive DESI, are briefly discussed. The capabilities of LS-DESI extend and/or complement the utilities of traditional DESI and electrospray ionization and will find extensive and valuable analytical application in the future.
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Affiliation(s)
- Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701;
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701;
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17
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Khakinejad M, Kondalaji SG, Donohoe GC, Valentine SJ. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 3. Estimating Surface Area Exposure by Deuterium Uptake. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:462-73. [PMID: 26620531 PMCID: PMC4872623 DOI: 10.1007/s13361-015-1305-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 05/17/2023]
Abstract
Gas-phase hydrogen deuterium exchange (HDX), collision cross section (CCS) measurement, and molecular dynamics simulation (MDS) techniques were utilized to develop and compare three methods for estimating the relative surface area exposure of separate peptide chains within bovine insulin ions. Electrosprayed [M - 3H](3-) and [M - 5H](5-) insulin ions produced a single conformer type with respective collision cross sections of 528 ± 5 Å(2) and 808 ± 2 Å(2). [M - 4H](4-) ions were comprised of more compact (Ω = 676 ± 3 Å(2)) and diffuse (i.e., more elongated, Ω = 779 ± 3 Å(2)) ion conformer types. Ions were subjected to HDX in the drift tube using D2O as the reagent gas. Collision-induced dissociation was used to fragment mobility-selected, isotopically labeled [M - 4H](4-) and [M - 5H](5-) ions into the protein subchains. Deuterium uptake levels of each chain can be explained by limited inter-chain isotopic scrambling upon collisional activation. Using nominal ion structures from MDS and a hydrogen accessibility model, the deuterium uptake for each chain was correlated to its exposed surface area. In separate experiments, the per-residue deuterium content for the protonated and deprotonated ions of the synthetic peptide KKDDDDDIIKIIK were compared. The differences in deuterium content indicated the regional HDX accessibility for cations versus anions. Using ions of similar conformational type, this comparison highlights the complementary nature of HDX data obtained from positive- and negative-ion analysis.
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Affiliation(s)
- Mahdiar Khakinejad
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | | | - Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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18
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Wright PA, Alex A, Pullen FS. Can computational chemistry be used to predict CID fragmentation of anions? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2309-2315. [PMID: 26522325 DOI: 10.1002/rcm.7394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/10/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Affiliation(s)
| | - Alexander Alex
- Evenor Consulting Ltd, The New Barn, Mill Lane, Eastry, UK
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19
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Sohn CH, Gao J, Thomas DA, Kim TY, Goddard WA, Beauchamp JL. Mechanisms and energetics of free radical initiated disulfide bond cleavage in model peptides and insulin by mass spectrometry. Chem Sci 2015; 6:4550-4560. [PMID: 29142703 PMCID: PMC5666513 DOI: 10.1039/c5sc01305d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/20/2015] [Indexed: 11/21/2022] Open
Abstract
We investigate the mechanism of disulfide bond cleavage in gaseous peptide and protein ions initiated by a covalently-attached regiospecific acetyl radical using mass spectrometry (MS). Highly selective S-S bond cleavages with some minor C-S bond cleavages are observed by a single step of collisional activation. We show that even multiple disulfide bonds in intact bovine insulin are fragmented in the MS2 stage, releasing the A- and B-chains with a high yield, which has been challenging to achieve by other ion activation methods. Yet, regardless of the previous reaction mechanism studies, it has remained unclear why (1) disulfide bond cleavage is preferred to peptide backbone fragmentation, and why (2) the S-S bond that requires the higher activation energy conjectured in previously suggested mechanisms is more prone to be cleaved than the C-S bond by hydrogen-deficient radicals. To probe the mechanism of these processes, model peptides possessing deuterated β-carbon(s) at the disulfide bond are employed. It is suggested that the favored pathway of S-S bond cleavage is triggered by direct acetyl radical attack at sulfur with concomitant cleavage of the S-S bond (SH2). The activation energy for this process is substantially lower by ∼9-10 kcal mol-1 than those of peptide backbone cleavage processes determined by density functional quantum chemical calculations. Minor reaction pathways are initiated by hydrogen abstraction from the α-carbon or the β-carbon of a disulfide, followed by β-cleavages yielding C-S or S-S bond scissions. The current mechanistic findings should be generally applicable to other radical-driven disulfide bond cleavages with different radical species such as the benzyl and methyl pyridyl radicals.
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Affiliation(s)
- Chang Ho Sohn
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Jinshan Gao
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Daniel A Thomas
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Tae-Young Kim
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - William A Goddard
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
- Materials and Process Simulation Center , Beckman Institute , California Institute of Technology , Pasadena , CA 91125 , USA
| | - J L Beauchamp
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
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20
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21
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Nguyen HTH, Shaffer CJ, Ledvina AR, Coon JJ, Tureček F. Serine effects on collision-induced dissociation and photodissociation of peptide cation radicals of the z+• -type. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 378:20-30. [PMID: 26005367 PMCID: PMC4437545 DOI: 10.1016/j.ijms.2014.06.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The serine residue displays specific effects on the dissociations of peptide fragment cation-radicals of the z+• type which are produced by electron transfer dissociation. Energy-resolved collision-induced dissociation (ER-CID), time-resolved infrared multiphoton dissociation (TR-IRMPD), and single-photon UV photodissociation at 355 nm revealed several competitive dissociation pathways consisting of loss of OH radical, water, and backbone cleavages occurring at N-terminal and C-terminal positions relative to the serine residue. The activation modes using slow-heating and UV photon absorption resulted in different relative intensities of fragment ions. This indicated that the dissociations proceeded through several channels with different energy-dependent kinetics. The experimental data were interpreted with the help of electron structure calculations that provided fully optimized structures and relative energies for cis and trans amide isomers of the z4+• ions as well as isomerization, dissociation, and transition state energies. UV photon absorption by the z4+• ions was due to Cα-radical amide groups created by ETD that provided a new chromophore absorbing at 355 nm.
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Affiliation(s)
- Huong T H Nguyen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA, 98195-1700
| | - Christopher J Shaffer
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA, 98195-1700
| | - Aaron R Ledvina
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin, Madison, WI, USA ; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA, 98195-1700
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22
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Tran TTN, Brinkworth CS, Bowie JH. The identification of disulfides in ricin D using proteolytic cleavage followed by negative-ion nano-electrospray ionization mass spectrometry of the peptide fragments. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:182-190. [PMID: 25641493 DOI: 10.1002/rcm.7088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/30/2014] [Accepted: 10/30/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE To use negative-ion nano-electrospray ionization mass spectrometry of peptides from the tryptic digest of ricin D, to provide sequence information; in particular, to identify disulfide position and connectivity. METHODS Negative-ion fragmentations of peptides from the tryptic digest of ricin D was studied using a Waters QTOF2 mass spectrometer operating in MS and MS(2) modes. RESULTS Twenty-three peptides were obtained following high-performance liquid chromatography and studied by negative-ion mass spectrometry covering 73% of the amino-acid residues of ricin D. Five disulfide-containing peptides were identified, three intermolecular and two intramolecular disulfide-containing peptides. The [M-H](-) anions of the intermolecular disulfides undergo facile cleavage of the disulfide units to produce fragment peptides. In negative-ion collision-induced dissociation (CID) these source-formed anions undergo backbone cleavages, which provide sequencing information. The two intramolecular disulfides were converted proteolytically into intermolecular disulfides, which were identified as outlined above. CONCLUSIONS The positions of the five disulfide groups in ricin D may be determined by characteristic negative-ion cleavage of the disulfide groups, while sequence information may be determined using the standard negative-ion backbone cleavages of the resulting cleaved peptides. Negative-ion mass spectrometry can also be used to provide partial sequencing information for other peptides (i.e. those not containing Cys) using the standard negative-ion backbone cleavages of these peptides.
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Affiliation(s)
- T T Nha Tran
- Department of Chemistry, The University of Adelaide, South Australia, Australia, 5005
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23
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Cai Y, Zheng Q, Liu Y, Helmy R, Loo JA, Chen H. Integration of electrochemistry with ultra-performance liquid chromatography/mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:341-51. [PMID: 26307715 PMCID: PMC4552337 DOI: 10.1255/ejms.1318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
This study presents the development of ultra-performance liquid chromatography (UPLC) mass spectrometry (MS) combined with electrochemistry (EC) for the first time and its application for the structural analysis of proteins/peptides that contain disulfide bonds. In our approach, a protein/peptide mixture sample undergoes a fast UPLC separation and subsequent electrochemical reduction in an electrochemical flow cell followed by online MS and tandem mass spectrometry (MS/MS) analyses. The electrochemical cell is coupled to the mass spectrometer using our recently developed desorption electrospray ionization (DESI) interface. Using this UPLC/EC/DESI-MS method, peptides that contain disulfide bonds can be differentiated from those without disulfide bonds, as the former are electroactive and reducible. MS/MS analysis of the disulfide-reduced peptide ions provides increased information on the sequence and disulfide-linkage pattern. In a reactive DESI- MS detection experiment in which a supercharging reagent was used to dope the DESI spray solvent, increased charging was obtained for the UPLC-separated proteins. Strikingly, upon online electrolytic reduction, supercharged proteins (e.g., α-lactalbumin) showed even higher charging, which will be useful in top- down protein structure MS analysis as increased charges are known to promote protein ion dissociation. Also, the separation speed and sensitivity are enhanced by approximately 1(~)2 orders of magnitude by using UPLC for the liquid chromatography (LC)/EC/MS platform, in comparison to the previously used high- performance liquid chromatography (HPLC). This UPLC/EC/DESI-MS method combines the power of fast UPLC separation, fast electrochemical conversion, and online MS structural analysis for a potentially valuable tool for proteomics research and bioanalysis.
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Affiliation(s)
- Yi Cai
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701 USA.
| | - Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701 USA.
| | - Yong Liu
- Department of Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., Rahway, NJ 07065, USA.
| | - Roy Helmy
- Department of Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., Rahway, NJ 07065, USA.
| | - Joseph A Loo
- Dep artment of Chemistry and Biochemistry, Department of Biological Chemistry, David Geffen School of Medicine at UCLA, and UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA 90095, USA.
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701 USA.
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24
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Zheng Q, Zhang H, Tong L, Wu S, Chen H. Cross-linking electrochemical mass spectrometry for probing protein three-dimensional structures. Anal Chem 2014; 86:8983-91. [PMID: 25141260 PMCID: PMC4165463 DOI: 10.1021/ac501526n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/20/2014] [Indexed: 12/27/2022]
Abstract
Chemical cross-linking combined with mass spectrometry (MS) is powerful to provide protein three-dimensional structure information but difficulties in identifying cross-linked peptides and elucidating their structures limit its usefulness. To tackle these challenges, this study presents a novel cross-linking MS in conjunction with electrochemistry using disulfide-bond-containing dithiobis[succinimidyl propionate] (DSP) as the cross-linker. In our approach, electrolysis of DSP-bridged protein/peptide products, as online monitored by desorption electrospray ionization mass spectrometry is highly informative. First, as disulfide bonds are electrochemically reducible, the cross-links are subject to pronounced intensity decrease upon electrolytic reduction, suggesting a new way to identify cross-links. Also, mass shift before and after electrolysis suggests the linkage pattern of cross-links. Electrochemical reduction removes disulfide bond constraints, possibly increasing sequence coverage for tandem MS analysis and yielding linear peptides whose structures are more easily determined than their cross-linked precursor peptides. Furthermore, this cross-linking electrochemical MS method is rapid, due to the fast nature of electrochemical conversion (much faster than traditional chemical reduction) and no need for chromatographic separation, which would be of high value for structural proteomics research.
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Affiliation(s)
- Qiuling Zheng
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States
| | - Hao Zhang
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Lingying Tong
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States
| | - Shiyong Wu
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States
| | - Hao Chen
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States
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25
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Guo M, Pan Y, Zhang R, Cao Y, Chen J, Pan Y. The specific cleavage of lactone linkage to open-loop in cyclic lipopeptide during negative ESI tandem mass spectrometry: the hydrogen bond interaction effect of 4-ethyl guaiacol. PLoS One 2014; 9:e104835. [PMID: 25144459 PMCID: PMC4140680 DOI: 10.1371/journal.pone.0104835] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/13/2014] [Indexed: 11/27/2022] Open
Abstract
Mass spectrometry is a valuable tool for the analysis and identification of chemical compounds, particularly proteins and peptides. Lichenysins G, the major cyclic lipopeptide of lichenysin, and the non-covalent complex of lichenysins G and 4-ethylguaiacol were investigated with negative ion ESI tandem mass spectrometry. The different fragmentation mechanisms for these compounds were investigated. Our study shows the 4-ethylguaiacol hydrogen bond with the carbonyl oxygen of the ester group in the loop of lichenysins G. With the help of this hydrogen bond interaction, the ring structure preferentially opens in lactone linkage rather than O-C bond of the ester-group to produce alcohol and ketene. Isothermal titration 1H-NMR analysis verified the hydrogen bond and determined the proportion of subject and ligand in the non-covalent complex to be 1∶1. Theoretical calculations also suggest that the addition of the ligand can affect the energy of the transition structures (TS) during loop opening.
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Affiliation(s)
- Mengzhe Guo
- Department of Chemistry, Zhejiang University, Hangzhou, China
| | - Youlu Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Rong Zhang
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yang Cao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jianzhong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, China
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Nishikaze T, Kawabata SI, Tanaka K. Fragmentation characteristics of deprotonated N-linked glycopeptides: influences of amino acid composition and sequence. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:988-98. [PMID: 24664808 DOI: 10.1007/s13361-014-0854-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 05/12/2023]
Abstract
Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., (2,4)AR, (2,4)AR-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + (0,2)X0-H](-) and [peptide-NH3-H](-)). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides.
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Affiliation(s)
- Takashi Nishikaze
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Nakagyo-ku, Kyoto, Japan,
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27
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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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28
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Smith SA, Kalcic CL, Cui L, Reid GE. Femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) of deprotonated phosphopeptide anions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2807-2817. [PMID: 24214867 DOI: 10.1002/rcm.6750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Radical-directed dissociation techniques provide structural information which is complementary to that from conventional collision-induced dissociation (CID). The analysis of phosphopeptide anions is warranted due to their relatively acidic character. As femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) is uniquely initiated by field ionization, an investigation is warranted to determine whether fsLID may provide novel analytical utility for phosphopeptide anions. METHODS Twenty-three synthetic deprotonated phosphopeptide anions were introduced into a three-dimensional quadrupole ion trap mass spectrometer via electrospray ionization. The ion trap was interfaced with a near-IR (802 nm) ultrashort-pulsed (35 fs FWHM) ultrahigh-powered (peak power ~10(14) W/cm(2)) laser system. Performance comparisons are made with other techniques applied to phosphopeptide anion analysis, including CID, electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), activated electron photodetachment dissociation (activated-EPD), and ultraviolet photodissociation (UVPD). RESULTS FsLID-MS/MS of multiply deprotonated phosphopeptide anions provides sequence information via phosphorylation-intact a/x ions in addition to other sequence ions, satellite ions, and side-chain losses. Novel fragmentation processes include selective c-ion formation N-terminal to Ser/Thr and a phosphorylation-specific correlation between xn -98 ion abundances and phosphorylation at the n(th) residue. Sequencing-quality data required about 30 s of signal averaging. fsLID-MS/MS of singly deprotonated phosphopeptides did not yield product anions with stable trajectories, despite significant depletion of the precursor. CONCLUSIONS Multiply deprotonated phosphopeptide anions were sequenced via negative-mode fsLID-MS/MS, with phosphosite localization facilitated by a/x ion series in addition to diagnostic x(n)-98 ions. fsLID-MS/MS is qualitatively competitive with other techniques. Further efficiency enhancements (e.g., implementation on a linear trap or/and higher pulse frequencies) may permit sequence analyses on chromatographic timescales.
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Affiliation(s)
- Scott A Smith
- RTSF Mass Spectrometry & Metabolomics Core, Michigan State University, East Lansing, MI, 48824, USA
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29
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Tran TTN, Wang T, Hack S, Bowie JH. Fragmentations of [M-H]- anions of peptides containing Ser sulfate. A joint experimental and theoretical study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2287-2296. [PMID: 24097384 DOI: 10.1002/rcm.6686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE To determine the negative-ion cleavages from [M-H](-) ions of Ser sulfate-containing peptides using experiment and theory in concert. METHODS Fragmentations were explored using a Waters QTOF2 mass spectrometer in negative-ion electrospray mode, together with calculations at the CAM-B3LYP/6-311++g(d,p) level of theory. Peptides used in this study were: GS(SO3H)(OH) 1 GS(SO3H)(OCH3) 1a GAVS(SO3H)(OH) 2 GAVS(SO3H)(OCH3) 2a GLS(SO3H)(GVA(OH) 3 GLS(SO3H)GDA(OH) 4 GLS(SO3H)GS(SO3H)A(OH) 5. RESULTS Previously, it has been shown that a peptide containing a Tyr sulfate group shows [(M-H)(-) -SO3] as the base peak. Only a small peak was observed corresponding to HOSO3(-) (formed following rearrangement of the sulfate). A Ser sulfate-containing peptide, in contrast, shows pronounced peaks due to cleavage product anions [(M-H)(-)-SO3] and HOSO3(-). Theoretical calculations at the CAM-B3LYP/6-311++g(d,p) level of theory suggest that rearrangement of a Ser sulfate to give C-terminal CO2SO3H is energetically unfavourable in comparison with fragmentation of the intact Ser sulfate to yield [(M-H)(-)-SO3] and HOSO3(-). [(M-H)(-)-H2SO4] anions are not observed in the spectra of peptides containing Ser sulfate, presumably because HOSO3(-) is a relatively weak gas-phase base (ΔGacid = 1265 kJ mol(-1)). CONCLUSIONS Experimental and theoretical data suggest that [(M-H)(-)-SO3] and HOSO3(-) product anions (from a peptide with a C-terminal Ser sulfate) are formed from the serine sulfate anion accompanied by specific proton transfer. CID MS/MS/MS data for an [(M-H)(-)-SO3] ion of an underivatised sulfate-containing peptide will normally allow the determination of the amino acid sequence of that peptide. The one case we have studied where that is not the case is GLS(SO3H)GDA(OH), where the peptide contains Ser sulfate and Asp, where the diagnostic Asp cleavages are competitive with the Ser sulfate cleavages.
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Affiliation(s)
- T T Nha Tran
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
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30
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Zheng Q, Zhang H, Chen H. Integration of online digestion and electrolytic reduction with mass spectrometry for rapid disulfide-containing protein structural analysis. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 353:84-92. [PMID: 25419170 PMCID: PMC4240030 DOI: 10.1016/j.ijms.2013.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bottom-up structural analysis of disulfide-bond containing proteins usually involves time-consuming offline enzymatic digestion, chemical reduction and thiol protection prior to mass spectrometric detection, which takes many hours. This paper presents an expedited bottom-up approach, employing desorption electrospray ionization-mass spectrometry (DESI-MS) coupled with online pepsin digestion and online electrochemical reduction of disulfide bonds. Peptides are generated in high digestion yield as its precursor protein in acidic aqueous solution flows through a pepsin column, which can undergo direct electrolysis. The electrolytic behaviors of peptides, as online monitored by DESI-MS, suggest the presence or absence of disulfide bonds in the peptides, and also provide information to relate disulfide bond-containing peptide precursors to their corresponding reduced products. Furthermore, selective electrolysis simply using different reduction potentials can be adopted to generate either partially or fully reduced peptides to assist disulfide bond mapping. In addition, it turns out that DESI is suitable for ionizing peptides in water without organic solvent additives (organic solvent additives would not be compatible with the use of pepsin column). The feasibility of this method was demonstrated using insulin, a protein carrying three pairs of disulfide-bonds as an example, in which all disulfide bond linkages and most of the protein sequence were successfully determined. Strikingly, this method shortens the sample digestion, reduction and MS detection from hours to less than 7 min, which could be of high value in high-throughput proteomics research.
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Affiliation(s)
- Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Hao Zhang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
- Corresponding author. Tel.: +1 314 935 7486
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Corresponding author. Tel.: +1 740 593 0719; fax: +1 740 597 3157
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31
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Goyder MS, Rebeaud F, Pfeifer ME, Kálmán F. Strategies in mass spectrometry for the assignment of Cys-Cys disulfide connectivities in proteins. Expert Rev Proteomics 2013; 10:489-501. [PMID: 24087910 DOI: 10.1586/14789450.2013.837663] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Elucidating disulfide linkage patterns is a crucial part of protein characterization, for which mass spectrometry (MS) is now an indispensable analytical tool. In many cases, MS-based disulfide connectivity assignment is straightforwardly achieved using one-step protein fragmentation in the unreduced form followed by mass measurement of bridged fragments. By contrast, venom proteins, which are receiving increasing interest as potential therapeutics, are a challenge for MS-based disulfide assignment due to their numerous closely spaced cysteines and knotted disulfide structure, requiring creative strategies to determine their connectivity. Today, these include the use of an array of reagents for enzymatic and/or chemical cleavage, partial reduction, differential cysteine labeling and tandem MS. This review aims to describe the toolkit of techniques available to MS users approaching both straightforward and complex disulfide bridge assignments, with a particular focus on strategies utilizing standard instrumentation found in a well-equipped analytical or proteomics laboratory.
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Affiliation(s)
- Miriam S Goyder
- Institute of Life Technologies, University of Applied Sciences Western Switzerland (HES-SO Valais/Wallis), 1950 Sion, Switzerland
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32
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Lu Z, Chai Y, Guo C, Sun C, Pan Y. H2O loss in the fragmentation of deprotonated N-o-tolylamides in tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1010-1014. [PMID: 24078241 DOI: 10.1002/jms.3257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 07/13/2013] [Accepted: 07/16/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Zhihua Lu
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
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33
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Samgina TY, Vorontsov EA, Gorshkov VA, Artemenko KA, Zubarev RA, Ytterberg JA, Lebedev AT. Collision-induced dissociation fragmentation inside disulfide C-terminal loops of natural non-tryptic peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1037-1044. [PMID: 23633018 DOI: 10.1007/s13361-013-0632-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 06/02/2023]
Abstract
Collision-induced dissociation (CID) spectra of long non-tryptic peptides are usually quite complicated and rather difficult to interpret. Disulfide bond formed by two cysteine residues at C-terminus of frog skin peptides precludes one to determine sequence inside the forming loop. Thereby, chemical modification of S-S bonds is often used in "bottom up" sequencing approach. However, low-energy CID spectra of natural non-tryptic peptides with C-terminal disulfide cycle demonstrate an unusual fragmentation route, which may be used to elucidate the "hidden" C-terminal sequence. Low charge state protonated molecules experience peptide bond cleavage at the N-terminus of C-terminal cysteine. The forming isomeric acyclic ions serve as precursors for a series of b-type ions revealing sequence inside former disulfide cycle. The reaction is preferable for peptides with basic lysine residues inside the cycle. It may also be activated by acidic protons of Asp and Glu residues neighboring the loop. The observed cleavages may be quite competitive, revealing the sequence inside disulfide cycle, although S-S bond rupture does not occur in this case.
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Affiliation(s)
- Tatiana Y Samgina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
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34
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Tran TTN, Wang T, Hack S, Bowie JH. Fragmentations of [M-H]- anions of peptides containing tyrosine sulfate. Does the sulfate group rearrange? A joint experimental and theoretical study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1135-1142. [PMID: 23592118 DOI: 10.1002/rcm.6547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/21/2013] [Accepted: 02/14/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE To investigate the fragmentations in the negative-ion electrospray mass spectra of peptides containing tyrosine sulfate. METHODS Possible fragmentation mechanisms were explored using a Waters QTOF2 tandem mass spectrometer in concert with calculations at the CAM-B3LYP/6-311++g(d,p) level of theory. RESULTS The major negative ion formed in the ESI-MS of peptides containing tyrosine sulfate is [(M-H)-SO3](-) and this process normally yields the base peak of the spectrum. The basic backbone cleavages of [(M-H)-SO3](-) allowed the sequence of the peptide to be determined. Rearrangement reactions involving the formation of HOSO3(-) and [(M-H)-H2SO4](-) yielded minor peaks with relative abundances ≤ 10% and ≤ 2%, respectively. CONCLUSIONS The mass spectra of the [M-H](-) and [(M-H)-SO3](-) anions of peptides containing tyrosine sulfate allowed the position of the tyrosine sulfate group to be determined, together with the amino acid sequence of the peptide.
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Affiliation(s)
- T T Nha Tran
- Department of Chemistry, The University of Adelaide, South Australia, Australia
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35
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Echterbille J, Quinton L, Gilles N, De Pauw E. Ion Mobility Mass Spectrometry as a Potential Tool To Assign Disulfide Bonds Arrangements in Peptides with Multiple Disulfide Bridges. Anal Chem 2013; 85:4405-13. [DOI: 10.1021/ac303686w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Julien Echterbille
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
| | - Loïc Quinton
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
| | - Nicolas Gilles
- iBiTec-S,
SIMOPRO, Commissariat à l’Energie Atomique, Gif-sur-Yvette,
France
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
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36
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Calabrese AN, Wang T, Bowie JH, Pukala TL. Negative ion fragmentations of disulfide-containing cross-linking reagents are competitive with aspartic acid side-chain-induced cleavages. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:238-248. [PMID: 23239338 DOI: 10.1002/rcm.6445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/14/2012] [Accepted: 10/18/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE It has been shown that the disulfide moiety in the chemical cross-linking reagent dithiobis(succinimidyl)propionate (DSP), which is similar in structure to the natural cystine disulfide, cleaves preferentially to the peptide backbone in the negative ion mode. However, the tandem mass (MS/MS) spectra of peptides in the negative ion mode are often dominated by products arising from low-energy, side-chain-induced processes, which may compete with any facile cross-linker fragmentations and complicate identification of chemical cross-links in a complex mixture. METHODS Two disulfide-containing crosslinking reagents similar to DSP, but with varying spacer arm lengths, were synthesized and the MS/MS spectra of several model peptides cross-linked with these reagents were investigated. Theoretical calculations were used to describe the energetics of the cross-linker fragmentations as well as several low-energy side-chain-induced fragmentations which compete with disulfide cleavages. RESULTS Altering the spacer arm length of the cross-linker, such that there is one methylene group less than in DSP, results in a more facile cleavage process, whilst the opposite is true when a methylene group is added. Of the low-energy side-chain-induced fragmentations studied, only those from aspartic acid compete significantly with those of the cross-linker disulfide. CONCLUSIONS Low-energy cleavage processes from aspartic acid that compete with cross-linker fragmentations occur in the negative ion MS/MS spectra of the cross-linked peptides, irrespective of the spacer arm length. Other fragmentation pathways do not significantly interfere with low-energy disulfide cleavage, making the presence of additional product ions in the MS/MS spectrum diagnostic for the presence of aspartic acid.
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Affiliation(s)
- Antonio N Calabrese
- School of Chemistry and Physics, The University of Adelaide, Adelaide, SA, Australia, 5005
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37
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Liu P, Lu M, Zheng Q, Zhang Y, Dewald HD, Chen H. Recent advances of electrochemical mass spectrometry. Analyst 2013; 138:5519-39. [DOI: 10.1039/c3an00709j] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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38
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Niessen WMA. Fragmentation of toxicologically relevant drugs in negative-ion liquid chromatography-tandem mass spectrometry. MASS SPECTROMETRY REVIEWS 2012; 31:626-665. [PMID: 22829116 DOI: 10.1002/mas.20359] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 03/13/2012] [Accepted: 03/13/2012] [Indexed: 06/01/2023]
Abstract
Negative-ion LC-MS analysis of drugs is applied far less frequently than positive-ion LC-MS. Data on the interpretation of negative-ion MS-MS spectra are even more scarce. Therefore, following the recent review on the class-specific fragmentation of toxicologically relevant compounds in positive-ion MS-MS, it was decided to perform a similar study in negative-ion MS-MS. To this end, a set of over 500 negative-ion MS-MS spectra was collected from three libraries applied in toxicological general unknown screening and systematic toxicological analysis. The compounds involved were classified by chemical and therapeutic class. The MS-MS spectra were manually interpreted and relevant interpretation data were searched for in the scientific literature. The emphasis in the discussion is on class-specific fragmentation, because discussing fragmentation of all individual compounds would take far too much space. Negative-ion MS-MS fragmentation is discussed for a wide variety of toxicologically relevant compounds, including dihydropyridine calcium channel blockers, diuretics, barbiturates, anti-inflammatory drugs, anti-diabetics, sulfonamide and betalactam antibiotics, and a number of classes of pesticides.
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Affiliation(s)
- W M A Niessen
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands.
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39
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Bokatzian-Johnson SS, Stover ML, Dixon DA, Cassady CJ. A comparison of the effects of amide and acid groups at the C-terminus on the collision-induced dissociation of deprotonated peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1544-1557. [PMID: 22833234 DOI: 10.1007/s13361-012-0431-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 05/10/2012] [Accepted: 06/12/2012] [Indexed: 06/01/2023]
Abstract
The dissociative behavior of peptide amides and free acids was explored using low-energy collision-induced dissociation and high level computational theory. Both positive and negative ion modes were utilized, but the most profound differences were observed for the deprotonated species. Deprotonated peptide amides produce a characteristic c(m-2)(-) product ion (where m is the number of residues in the peptide) that is either absent or in low abundance in the analogous peptide acid spectrum. Peptide acids show an enhanced formation of c(m-3)(-); however, this is not generally as pronounced as c(m-2)(-) production from amides. The most notable occurrence of an amide-specific product ion is for laminin amide (YIGSR-NH(2)) and this case was investigated using several modified peptides. Mechanisms involving 6- and 9-membered ring formation were proposed, and their energetic properties were investigated using G3(MP2) molecular orbital theory calculations. For example, with C-terminal deprotonation of pentaglycine amide, formation of c(m-2)(-) and a 6-membered ring diketopiperazine neutral requires >31.6 kcal/mol, which is 26.1 kcal/mol less than the analogous process involving the peptide acid. The end group specific fragmentation of peptide amides in the negative ion mode may be useful for identifying such groups in proteomic applications.
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40
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Bowie JH, Separovic F, Tyler MJ. Host-defense peptides of Australian anurans. Part 2. Structure, activity, mechanism of action, and evolutionary significance. Peptides 2012; 37:174-88. [PMID: 22771617 DOI: 10.1016/j.peptides.2012.06.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 06/26/2012] [Accepted: 06/26/2012] [Indexed: 01/01/2023]
Abstract
A previous review summarized research prior to 2004 carried out on the bioactive host-defense peptides contained in the skin secretions of Australian anurans (frogs and toads). This review covers the extension of that research from 2004 to 2012, and includes membrane-active peptides (including antibacterial, anticancer, antifungal and antiviral peptides) together with the mechanisms by which these peptides interact with model membranes, peptides that may be classified as "neuropeptides" (including smooth muscle active peptides, opioids and immunomodulators) and peptides which inhibit the formation of nitric oxide from neuronal nitric oxide synthase. The review discusses the outcome of cDNA sequencing of signal-spacer-active peptides from an evolutionary viewpoint, and also lists those peptides for which activities have not been found to this time.
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Affiliation(s)
- John H Bowie
- Department of Chemistry, School of Chemistry and Physics, The University of Adelaide, South Australia 5005, Australia.
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41
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Wang T, Tran TTN, Calabrese AN, Bowie JH. Backbone fragmentations of [M-H]- anions from peptides. Reinvestigation of the mechanism of the beta prime cleavage. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1832-1840. [PMID: 22777785 DOI: 10.1002/rcm.6297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE An experimental study has shown that the structure of a β' ion proposed earlier is incorrect. Backbone cleavage β' anions have structures R(NH(-)) from systems [[RNHCH(X)CONHCH(Y)CO(2)H (or C-terminal CONH(2))-H](-) (where R is the rest of the peptide molecule and X and Y represent the α side chains of the individual amino acid residues). METHODS Ab initio calculations were carried out at the CAM-B3LYP/6-311++g(d,p) level of theory. CONCLUSIONS The calculations suggest that RNH(-) ions are formed by S(N)i cyclisation processes involving either (i) the C-terminal CO(2)(-) or C-terminal [CONH](-) as appropriate, or (ii) an enolate ion [-NHC(-)(Y)-] cyclising at the backbone CH of the -CH(X)- group. Concomitant C-N bond cleavage then liberates an RNH(-) ion, processes which can occur along the peptide backbone.
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Affiliation(s)
- Tianfang Wang
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
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42
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Calabrese AN, Good NJ, Wang T, He J, Bowie JH, Pukala TL. A negative ion mass spectrometry approach to identify cross-linked peptides utilizing characteristic disulfide fragmentations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1364-1375. [PMID: 22644737 DOI: 10.1007/s13361-012-0407-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/29/2012] [Accepted: 04/30/2012] [Indexed: 06/01/2023]
Abstract
Chemical cross-linking combined with mass spectrometry (MS) is an analytical tool used to elucidate the topologies of proteins and protein complexes. However, identification of the low abundance cross-linked peptides and modification sites amongst a large quantity of proteolytic fragments remains challenging. In this work, we present a strategy to identify cross-linked peptides by negative ion MS for the first time. This approach is based around the facile cleavages of disulfide bonds in the negative mode, and allows identification of cross-linked products based on their characteristic fragmentations. MS(3) analysis of the cross-linked peptides allows for their sequencing and identification, with residue specific location of cross-linking sites. We demonstrate the applicability of the commercially available cystine based cross-linking reagent dithiobis(succinimidyl) propionate (DSP) and identify cross-linked peptides from ubiquitin. In each instance, the characteristic fragmentation behavior of the cross-linked species is described. The data presented here indicate that this negative ion approach may be a useful tool to characterize the structures of proteins and protein complexes, and provides the basis for the development of high throughput negative ion MS chemical cross-linking strategies.
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Affiliation(s)
- Antonio N Calabrese
- School of Chemistry and Physics, The University of Adelaide, Adelaide, SA, 5005, Australia
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43
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Hersberger KE, Håkansson K. Characterization of O-sulfopeptides by negative ion mode tandem mass spectrometry: superior performance of negative ion electron capture dissociation. Anal Chem 2012; 84:6370-7. [PMID: 22770115 DOI: 10.1021/ac301536r] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Positive ion mode collision-activated dissociation tandem mass spectrometry (CAD MS/MS) of O-sulfopeptides precludes determination of sulfonated sites due to facile proton-driven loss of the highly labile sulfonate groups. A previously proposed method for localizing peptide and protein O-sulfonation involves derivatization of nonsulfonated tyrosines followed by positive ion CAD MS/MS of the corresponding modified sulfopeptides for diagnostic sulfonate loss. This indirect method relies upon specific and complete derivatization of nonsulfonated tyrosines. Alternative MS/MS activation methods, including positive ion metastable atom-activated dissociation (MAD) and metal-assisted electron transfer dissociation (ETD) or electron capture dissociation (ECD) provide varying degrees of sulfonate retention. Sulfonate retention has also been reported following negative ion MAD and electron detachment dissociation (EDD), which also operates in negative ion mode in which sulfonate groups are less labile than in positive ion mode. However, an MS/MS activation technique that can effectively preserve sulfonate groups while providing extensive backbone fragmentation (translating to sequence information, including sulfonated sites) with little to no noninformative small molecule neutral loss has not previously been realized. Here, we report that negative ion CAD, EDD, and negative ETD (NETD) result in sulfonate retention mainly at higher charge states with varying degrees of fragmentation efficiency and sequence coverage. Similar to previous observations from CAD of sulfonated glycosaminoglycan anions, higher charge states translate to a higher probability of deprotonation at the sulfonate groups thus yielding charge-localized fragmentation without loss of the sulfonate groups. However, consequently, higher sulfonate retention comes at the price of lower sequence coverage in negative ion CAD. Fragmentation efficiency/sequence coverage averaged 19/6% and 33/20% in EDD and NETD, respectively, both of which are only applicable to multiply-charged anions. In contrast, the recently introduced negative ion ECD showed an average fragmentation efficiency of 69% and an average sequence coverage of 82% with complete sulfonate retention from singly- and doubly-deprotonated sulfopeptide anions.
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Affiliation(s)
- Katherine E Hersberger
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
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Zhang Y, Cui W, Zhang H, Dewald HD, Chen H. Electrochemistry-assisted top-down characterization of disulfide-containing proteins. Anal Chem 2012; 84:3838-42. [PMID: 22448817 DOI: 10.1021/ac300106y] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covalent disulfide bond linkage in a protein represents an important challenge for mass spectrometry (MS)-based top-down protein structure analysis as it reduces the backbone cleavage efficiency for MS/MS dissociation. This study presents a strategy for solving this critical issue via integrating electrochemistry (EC) online with a top-down MS approach. In this approach, proteins undergo electrolytic reduction in an electrochemical cell to break disulfide bonds and then undergo online ionization into gaseous ions for analysis by electron-capture dissociation (ECD) and collision-induced dissociation (CID). The electrochemical reduction of proteins allows one to remove disulfide bond constraints and also leads to increased charge numbers of the resulting protein ions. As a result, sequence coverage was significantly enhanced, as exemplified by β-lactoglobulin A (24 vs 75 backbone cleavages before and after electrolytic reduction, respectively) and lysozyme (5 vs 66 backbone cleavages before and after electrolytic reduction, respectively). This methodology is fast and does not need chemical reductants, which would have an important impact in high-throughput proteomics research.
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Affiliation(s)
- Yun Zhang
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, United States
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45
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Rumachik NG, McAlister GC, Russell JD, Bailey DJ, Wenger CD, Coon JJ. Characterizing peptide neutral losses induced by negative electron-transfer dissociation (NETD). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:718-27. [PMID: 22290482 PMCID: PMC3371390 DOI: 10.1007/s13361-011-0331-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 12/23/2011] [Accepted: 12/25/2011] [Indexed: 05/10/2023]
Abstract
We implemented negative electron-transfer dissociation (NETD) on a hybrid ion trap/Orbitrap mass spectrometer to conduct ion/ion reactions using peptide anions and radical reagent cations. In addition to sequence-informative ladders of a•- and x-type fragment ions, NETD generated intense neutral loss peaks corresponding to the entire or partial side-chain cleavage from amino acids constituting a given peptide. Thus, a critical step towards the characterization of this recently introduced fragmentation technique is a systematic study of synthetic peptides to identify common neutral losses and preferential fragmentation pathways. Examining 46 synthetic peptides with high mass accuracy and high resolution analysis permitted facile determination of the chemical composition of each neutral loss. We identified 19 unique neutral losses from 14 amino acids and three modified amino acids, and assessed the specificity and sensitivity of each neutral loss using a database of 1542 confidently identified peptides generated from NETD shotgun experiments employing high-pH separations and negative electrospray ionization. As residue-specific neutral losses indicate the presence of certain amino acids, we determined that many neutral losses have potential diagnostic utility. We envision this catalogue of neutral losses being incorporated into database search algorithms to improve peptide identification specificity and to further advance characterization of the acidic proteome.
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Affiliation(s)
- Neil G. Rumachik
- Departments of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | - Jason D. Russell
- Departments of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Derek J. Bailey
- Departments of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Craig D. Wenger
- Departments of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Joshua J. Coon
- Departments of Chemistry, University of Wisconsin, Madison, WI 53706, USA
- Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI 53706, USA
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46
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Lu M, Wolff C, Cui W, Chen H. Investigation of some biologically relevant redox reactions using electrochemical mass spectrometry interfaced by desorption electrospray ionization. Anal Bioanal Chem 2012; 403:355-65. [PMID: 22237914 PMCID: PMC3731448 DOI: 10.1007/s00216-011-5679-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/12/2011] [Accepted: 12/18/2011] [Indexed: 10/14/2022]
Abstract
Recently we have shown that, as a versatile ionization technique, desorption electrospray ionization (DESI) can serve as a useful interface to combine electrochemistry (EC) with mass spectrometry (MS). In this study, the EC/DESI-MS method has been further applied to investigate some aqueous phase redox reactions of biological significance, including the reduction of peptide disulfide bonds and nitroaromatics as well as the oxidation of phenothiazines. It was found that knotted/enclosed disulfide bonds in the peptides apamin and endothelin could be electrochemically cleaved. Subsequent tandem MS analysis of the resulting reduced peptide ions using collision-induced dissociation (CID) and electron-capture dissociation (ECD) gave rise to extensive fragment ions, providing a fast protocol for sequencing peptides with complicated disulfide bond linkages. Flunitrazepam and clonazepam, a class of nitroaromatic drugs, are known to undergo reduction into amines which was proposed to involve nitroso and N-hydroxyl intermediates. Now in this study, these corresponding intermediate ions were successfully intercepted and their structures were confirmed by CID. This provides mass spectrometric evidence for the mechanism of the nitro to amine conversion process during nitroreduction, an important redox reaction involved in carcinogenesis. In addition, the well-known oxidation reaction of chlorpromazine was also examined. The putative transient one-electron transfer product, the chlorpromazine radical cation (m/z 318), was captured by MS, for the first time, and its structure was also verified by CID. In addition to these observations, some features of the DESI-interfaced electrochemical mass spectrometry were discussed, such as simple instrumentation and the lack of background signal. These results further demonstrate the feasibility of EC/DESI-MS for the study of the biology-relevant redox chemistry and would find applications in proteomics and drug development research.
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Affiliation(s)
- Mei Lu
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Chloe Wolff
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Weidong Cui
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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Stover ML, Jackson VE, Matus MH, Adams MA, Cassady CJ, Dixon DA. Fundamental Thermochemical Properties of Amino Acids: Gas-Phase and Aqueous Acidities and Gas-Phase Heats of Formation. J Phys Chem B 2012; 116:2905-16. [DOI: 10.1021/jp207271p] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michele L. Stover
- Chemistry
Department, The University of Alabama, Shelby Hall, Box 870336,
Tuscaloosa, Alabama 35487-0336, United States
| | - Virgil E. Jackson
- Chemistry
Department, The University of Alabama, Shelby Hall, Box 870336,
Tuscaloosa, Alabama 35487-0336, United States
| | - Myrna H. Matus
- Chemistry
Department, The University of Alabama, Shelby Hall, Box 870336,
Tuscaloosa, Alabama 35487-0336, United States
| | - Margaret A. Adams
- Chemistry
Department, The University of Alabama, Shelby Hall, Box 870336,
Tuscaloosa, Alabama 35487-0336, United States
| | - Carolyn J. Cassady
- Chemistry
Department, The University of Alabama, Shelby Hall, Box 870336,
Tuscaloosa, Alabama 35487-0336, United States
| | - David A. Dixon
- Chemistry
Department, The University of Alabama, Shelby Hall, Box 870336,
Tuscaloosa, Alabama 35487-0336, United States
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Stutzman JR, Hassell KM, McLuckey SA. Dissociation Behavior of Tryptic and Intramolecular Disulfide-linked Peptide Ions Modified in the Gas Phase via Ion/Ion Reactions. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 312:195-200. [PMID: 22408389 PMCID: PMC3297198 DOI: 10.1016/j.ijms.2011.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Protonated tryptic peptides, somatostatin-14, and oxytocin have been subjected to reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas phase. The major product is a negatively-charged complex comprised of the peptide and the reagent. Upon dehydration of the complex, all peptides show evidence for Schiff base formation involving a primary amine of the peptide. Some peptides also show evidence for the formation of a relatively strong electrostatic interaction without Schiff base formation (i.e., a mixture of isomeric precursor ions is generated upon dehydration of the complex). Ion trap collision-induced dissociation of the dehydration products from all peptides examined gave distinct product ion spectra relative to the deprotonated and protonated forms of the peptides. The distinct behavior of the modified ions is attributed to the highly stable charge carrying sulfonate group, which tends to inhibit intramolecular proton transfer in negatively charged species. Modified anions of the peptides with an intramolecular disulfide linkage show evidence for cleavage of both the disulfide linkage and an amide bond in the loop defined by the disulfide bond. Modification of protonated peptides via charge inversion with FBDSA is a useful means for generating novel and distinct ion-types that can provide complementary structural information upon subsequent activation to that obtained from dissociation of protonated or deprotonated forms of the peptide.
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Affiliation(s)
| | | | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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Tran TTN, Wang T, Hack S, Hoffmann P, Bowie JH. Can collision-induced negative-ion fragmentations of [M-H](-) anions be used to identify phosphorylation sites in peptides? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3537-3548. [PMID: 22095502 DOI: 10.1002/rcm.5261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A joint experimental and theoretical investigation of the fragmentation behaviour of energised [M-H](-) anions from selected phosphorylated peptides has confirmed some of the most complex rearrangement processes yet to be reported for peptide negative ions. In particular: pSer and pThr (like pTyr) may transfer phosphate groups to C-terminal carboxyl anions and to the carboxyl anion side chains of Asp and Glu, and characteristic nucleophilic/cleavage reactions accompany or follow these rearrangements. pTyr may transfer phosphate to the side chains of Ser and Thr. The reverse reaction, namely transfer of a phosphate group from pSer or pThr to Tyr, is energetically unfavourable in comparison. pSer can transfer phosphate to a non-phosphorylated Ser. The non-rearranged [M-H](-) species yields more abundant product anions than its rearranged counterpart. If a peptide containing any or all of Ser, Thr and Tyr is not completely phosphorylated, negative-ion cleavages can determine the number of phosphated residues, and normally the positions of Ser, Thr and Tyr, but not which specific residues are phosphorylated. This is in accord with comments made earlier by Lehmann and coworkers.
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Affiliation(s)
- T T Nha Tran
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia
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Wang T, Tran TTN, Scanlon D, Andreazza HJ, Abell AD, Bowie JH. Diagnostic di- and triphosphate cyclisation in the negative ion electrospray mass spectra of phosphoSer peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:2649-2656. [PMID: 23657960 DOI: 10.1002/rcm.5171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 06/30/2011] [Accepted: 07/01/2011] [Indexed: 06/02/2023]
Abstract
It has been shown previously that [M-H](-) anions of small peptides containing two phosphate residues undergo cyclisation of the phosphate groups, following collision-induced dissociation (CID), to form a characteristic singly charged anion A (H3P2O7(-), m/z 177). In the present study it is shown that the precursor anions derived from the diphosphopeptides of caerin 1.1 [GLLSVLGSVAKHVLPHVVPVIAEHL(NH2)] and frenatin 3 [GLMSVLGHAVGNVLGGLFKPKS(OH)] also form the characteristic product anion A (m/z 177). Both of the precursor peptides show random structures in water, but partial helices in membrane-mimicking solvents [e.g. in d3-trifluoroethanol/water (1:1)]. In both cases the diphosphopeptide precursor anions must have flexible conformations in order to allow approach of the phosphate groups with consequent formation of A: for example, the two pSer groups of 4,22-diphosphofrenatin 3 are seventeen residues apart. Finally, CID tandem mass spectrometric (MS/MS) data from the [M-H](-) anion of the model triphosphoSer-containing peptide GpSGLGpSGLGpSGL(OH) show the presence of both product anions A (m/z 177) and D (m/z 257, H4P3O10(-)). Ab initio calculations at the HF/6-31+G(d)//AM1 level of theory suggest that cyclisation of the three phosphate groups occurs by a stepwise cascade mechanism in an energetically favourable reaction (ΔG = -245 kJ mol(-1)) with a maximum barrier of +123 kJ mol(-1).
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Affiliation(s)
- Tianfang Wang
- Department of Chemistry, The University of Adelaide, South Australia, 5005
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