1
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Brandner S, Habeck T, Lermyte F. New Insights into the Intrinsic Electron-Based Dissociation Behavior of Cytochrome c Oligomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1908-1916. [PMID: 37227392 DOI: 10.1021/jasms.3c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Between 2003 and 2017, four reports were published that demonstrated the intrinsic ability of the native iron-containing proteins cytochrome c and ferritin to undergo radical-based backbone fragmentation in the gas phase without the introduction of exogenous electrons. For cytochrome c in particular, this effect has so far only been reported to occur in the ion source, preventing the in-depth study of reactions occurring after gas-phase isolation of specific precursors. Here, we report the first observation of this intrinsic native electron capture dissociation behavior after quadrupole isolation of specific charge states of the cytochrome c dimer and trimer, providing direct experimental support for key aspects of the mechanism proposed 20 years ago. Furthermore, we provide evidence that, in contrast to some earlier proposals, these oligomeric states are formed in bulk solution rather than during the electrospray ionization process and that the observed fragmentation site preferences can be rationalized through the structure and interactions within these native oligomers rather than the monomer. We also show that the observed fragmentation pattern─and indeed, whether or not fragmentation occurs─is highly sensitive to the provenance and history of the protein samples, to the extent that samples can show distinct fragmentation behavior despite behaving identically in ion mobility experiments. This rather underexplored method therefore represents an exquisitely sensitive conformational probe and will hopefully receive more attention from the biomolecular mass spectrometry community in the future.
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Affiliation(s)
- Sarah Brandner
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
| | - Tanja Habeck
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
| | - Frederik Lermyte
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
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2
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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3
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Nicolardi S, Kilgour DPA, Dolezal N, Drijfhout JW, Wuhrer M, van der Burgt YEM. Evaluation of Sibling and Twin Fragment Ions Improves the Structural Characterization of Proteins by Top-Down MALDI In-Source Decay Mass Spectrometry. Anal Chem 2020; 92:5871-5881. [PMID: 32212639 PMCID: PMC7178258 DOI: 10.1021/acs.analchem.9b05683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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Comprehensive determination
of primary sequence and identification
of post-translational modifications (PTMs) are key elements in protein
structural analysis. Various mass spectrometry (MS) based fragmentation
techniques are powerful approaches for mapping both the amino acid
sequence and PTMs; one of these techniques is matrix-assisted laser
desorption/ionization (MALDI), combined with in-source decay (ISD)
fragmentation and Fourier-transform ion cyclotron resonance (FT-ICR)
MS. MALDI-ISD MS protein analysis involves only minimal sample preparation
and does not require spectral deconvolution. The resulting MALDI-ISD
MS data is complementary to electrospray ionization-based MS/MS sequencing
readouts, providing knowledge on the types of fragment ions is available.
In this study, we evaluate the isotopic distributions of z′ ions in protein top-down MALDI-ISD FT-ICR mass spectra and
show why these distributions can deviate from theoretical profiles
as a result of co-occurring and isomeric z and y-NH3 ions. Two synthetic peptides, containing
either normal or deuterated alanine residues, were used to confirm
the presence and unravel the identity of isomeric z and y-NH3 fragment ions (“twins”).
Furthermore, two reducing MALDI matrices, namely 1,5-diaminonaphthalene
and N-phenyl-p-phenylenediamine
were applied that yield ISD mass spectra with different fragment ion
distributions. This study demonstrates that the relative abundance
of isomeric z and y-NH3 ions requires consideration for accurate and confident assignments
of z′ ions in MALDI-ISD FT-ICR mass spectra.
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Affiliation(s)
- Simone Nicolardi
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
| | - David P A Kilgour
- Department of Chemistry, Nottingham Trent University, Nottingham NG11 0JN, United Kingdom
| | - Natasja Dolezal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden 2333, ZA, The Netherlands
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4
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Williams JP, Morrison LJ, Brown JM, Beckman JS, Voinov VG, Lermyte F. Top-Down Characterization of Denatured Proteins and Native Protein Complexes Using Electron Capture Dissociation Implemented within a Modified Ion Mobility-Mass Spectrometer. Anal Chem 2020; 92:3674-3681. [PMID: 31999103 DOI: 10.1021/acs.analchem.9b04763] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Electron-based fragmentation methods have revolutionized biomolecular mass spectrometry, in particular native and top-down protein analysis. Here, we report the use of a new electromagnetostatic cell to perform electron capture dissociation (ECD) within a quadrupole/ion mobility/time-of-flight mass spectrometer. This cell was installed between the ion mobility and time-of-flight regions of the instrument, and fragmentation was fast enough to be compatible with mobility separation. The instrument was already fitted with electron transfer dissociation (ETD) between the quadrupole and mobility regions prior to modification. We show excellent fragmentation efficiency for denatured peptides and proteins without the need to trap ions in the gas phase. Additionally, we demonstrate native top-down backbone fragmentation of noncovalent protein complexes, leading to comparable sequence coverage to what was achieved using the instrument's existing ETD capabilities. Limited collisional ion activation of the hemoglobin tetramer before ECD was reflected in the observed fragmentation pattern, and complementary ion mobility measurements prior to ECD provided orthogonal evidence of monomer unfolding within this complex. The approach demonstrated here provides a powerful platform for both top-down proteomics and mass spectrometry-based structural biology studies.
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Affiliation(s)
- Jonathan P Williams
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Lindsay J Morrison
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Joseph S Beckman
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Valery G Voinov
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Frederik Lermyte
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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5
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Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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6
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Zhang Z, Vachet RW. Gas-Phase Protein Salt Bridge Stabilities from Collisional Activation and Electron Transfer Dissociation. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 420:51-56. [PMID: 29056866 PMCID: PMC5646825 DOI: 10.1016/j.ijms.2016.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The gas phase structures of several proteins have been studied by electron transfer dissociation (ETD) with and without prior collisional heating after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Without prior collisional heating, we find that ETD fragmentation is mostly limited to regions of the protein that are not spanned by the salt bridges known to form in solution. When protein ions are collisionally heated before ETD, new product ions are observed, and in almost all cases, these new ions arise from protein regions that are spanned by the salt bridges. Together these results confirm the existence of salt bridges in protein ions and demonstrate that a sufficient amount energy is required to disrupt these salt bridges in the gas phase. More interestingly, we also show that different salt bridges require different collisional activation voltages to be disrupted, suggesting that they have variable stabilities in the gas phase. These stabilities appear to be influenced by the gas-phase basicities of the involved residues and the presence of nearby charged residues. We also find that higher collisional activation voltages are needed to enable the formation of new product from sites spanned by multiple salt bridges.
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Affiliation(s)
| | - Richard W. Vachet
- Address: Department of Chemistry, LGRT 104, 710 N. Pleasant St., University of Massachusetts, Amherst, MA 01003,
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7
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Pepin R, Laszlo KJ, Marek A, Peng B, Bush MF, Lavanant H, Afonso C, Tureček F. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1647-60. [PMID: 27400696 PMCID: PMC5031493 DOI: 10.1007/s13361-016-1437-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 05/27/2016] [Accepted: 06/16/2016] [Indexed: 05/18/2023]
Abstract
Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Robert Pepin
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | - Kenneth J Laszlo
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bo Peng
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | - Matthew F Bush
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | - Helène Lavanant
- Laboratoire COBRA CNRS UMR 6014 & FR 3038, Université de Rouen, INSA de Rouen, Mont St Aignan Cedex, France
| | - Carlos Afonso
- Laboratoire COBRA CNRS UMR 6014 & FR 3038, Université de Rouen, INSA de Rouen, Mont St Aignan Cedex, France
| | - František Tureček
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA.
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8
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Compton PD, Fornelli L, Kelleher NL, Skinner OS. Probing Asymmetric Charge Partitioning of Protein Oligomers during Tandem Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:132-136. [PMID: 26692813 PMCID: PMC4673687 DOI: 10.1016/j.ijms.2015.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Dissociation of gaseous protein complexes produced by native electrospray often induces an asymmetric partitioning of charge between ejected subunits. We present a simple asymmetric charge partitioning factor (ACPF) to quantify the magnitude of asymmetry in this effect. When applied to monomer ejection from the cytochrome c dimer and β-amylase tetramer, we found that the ~60-70% of precursor charge ending up in the ejected monomers corresponds to ACPFs of 1.38 and 2.51, respectively. Further, we used site-specific fragmentation from electron transfer dissociation (ETD) to identify differences in fragmentation and characterize domains of secondary-structure present in the dimer, ejected monomers, and monomers obtained directly from electrospray ionization (ESI). We found evidence of structural changes between the dimer and ejected monomer, but also that the ejected monomer had a nearly identical set of fragment ions produced by ETD as the ESI monomer with the same charge state. Surprisingly, APCF values for ETD fragment ions generated directly from the dimer revealed that the fragments undergo asymmetric charge partitioning at over twice the magnitude of that observed for ejection of the monomer.
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Affiliation(s)
- Philip D. Compton
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, USA
| | - Luca Fornelli
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, USA
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, USA
| | - Owen S. Skinner
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, USA
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9
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Wong PSJ, Chen X, Deng L, Wang Z, Li W, Wong YLE, Chan TWD. Suppression of peptide ion dissociation under electron capture: role of backbone amide hydrogen. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1757-1764. [PMID: 26331925 DOI: 10.1002/rcm.7275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/07/2015] [Accepted: 07/11/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The electron capture dissociation (ECD) of proteins/peptides is affected by the nature and sequence of amino acid residues. Electron capture/transfer with no dissociation is an intriguing phenomenon that has occasionally been observed. We have previously identified that diarginated peptides enriched with glutamic acid residues were found to show suppression of backbone fragmentation. In this paper, we report the effect of geometrical parameters of a peptide, including chain length, conformation and amide hydrogen, on the suppression of ECD fragmentation using synthetic model peptides. METHODS Glycine containing model polypeptides were used to probe the mechanism. Molecular-mechanics was used to obtain the conformation of the precursor ions. The ECD experiments were performed on a Bruker APEX III 4.7 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. RESULTS Significant decreases in the intensities of the fragment ions were observed for the 23-mer polypeptide with only one E residue. This implied that the E:R ratio was no longer the sole determining factor for the occurrence of suppression effects. Results of conformational searches showed that there was a hydrogen-bonding 'ladder' formed in the 23-mer polypeptide, which was not found in the 15-mer peptide. Substituting the normal amino acid residues by the corresponding N-methylated amino acid residues in the model peptide, the suppression effect disappeared. CONCLUSIONS Our results indicate that survival of the intact reduced peptide ion after electron capture depends also on the length of the peptide. The amide hydrogen was critical in forming the resonance structure that suppressed the ECD fragmentation.
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Affiliation(s)
- P-S Joyce Wong
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| | - Xiangfeng Chen
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
- Shandong Academy of Sciences, Jinan, Shandong, P.R. China
| | - Liulin Deng
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Washington, USA
| | - Ze Wang
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| | - Wan Li
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| | - Y L Elaine Wong
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
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10
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Schennach M, Breuker K. Probing Protein Structure and Folding in the Gas Phase by Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1059-67. [PMID: 25868904 PMCID: PMC4475247 DOI: 10.1007/s13361-015-1088-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/19/2015] [Accepted: 01/27/2015] [Indexed: 05/11/2023]
Abstract
The established methods for the study of atom-detailed protein structure in the condensed phases, X-ray crystallography and nuclear magnetic resonance spectroscopy, have recently been complemented by new techniques by which nearly or fully desolvated protein structures are probed in gas-phase experiments. Electron capture dissociation (ECD) is unique among these as it provides residue-specific, although indirect, structural information. In this Critical Insight article, we discuss the development of ECD for the structural probing of gaseous protein ions, its potential, and limitations.
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Affiliation(s)
- Moritz Schennach
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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11
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Tsybin YO, Vvorobyev A, Zhurov KO, Laskay ÜA. On the use of electron capture rate constants to describe electron capture dissociation mass spectrometry of peptides. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:451-458. [PMID: 26307726 DOI: 10.1255/ejms.1370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Electron capture dissociation (ECD) tandem mass spectrometry (MS/MS) is a powerful analytical tool for peptide and protein structure analysis. The product ion abundance (PIA) distribution in ECD MS/MS is known to vary as a function of electron irradiation period. This variation complicates the development of a method of peptide identification by correlation of ECD MS/MS data with experimental and theoretical mass spectra. Here, we first develop a kinetic model to describe primary electron capture by peptide dications leading to product ion formation and secondary electron capture resulting in product ion neutralization. We apply the developed kinetic model to calculate product ion formation rate constants and electron capture rate constants of product ions from ECD mass spectra acquired using various electron irradiation periods. Contrary to ECD PIA distributions, the product ion formation rate constants are shown to be independent of electron irradiation period and, thus, may be employed to characterize ECD product ion formation more universally. The electron capture rate constants of product ions in ECD Fourier transform ion cyclotron resonance MS were found to correlate (with a correlation factor, R(2), of ca 0.9) with ion mobility cross sections of product ions in electron transfer dissociation. Finally, we demonstrate that the electron irradiation period influences the ratio of radical and even-electron c and z product ions.
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Affiliation(s)
- Yury O Tsybin
- Bi omolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Aleksey Vvorobyev
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Konstantin O Zhurov
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ünige A Laskay
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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12
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Zhurov KO, Wodrich MD, Corminboeuf C, Tsybin YO. Ping-pong protons: how hydrogen-bonding networks facilitate heterolytic bond cleavage in peptide radical cations. J Phys Chem B 2014; 118:2628-37. [PMID: 24555737 DOI: 10.1021/jp412123h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Electron capture and electron transfer dissociation (ECD/ETD) tandem mass spectrometry (MS/MS) are commonly employed techniques for biomolecular analysis. The ECD/ETD process predominately cleaves N-Cα peptide backbone bonds, leading to primary sequence information complementary to other mass spectrometry techniques. Despite frequent laboratory use, the mechanistic underpinnings surrounding N-Cα bond cleavage remain debated. While the majority of mechanisms assume a homolytic bond rupture, we recently showed that heterolytic cleavage is also thermodynamically viable. For a cleavage of this type to be feasible, the charge separation created upon breaking of the N-Cα backbone bond must be quickly annihilated. In this work, we show, using density functional computations, that specific hydrogen-bonding motifs and structural rearrangements involving proton transfers stabilize the transition state associated with heterolytic cleavage and eliminate the ensuing charge separation from the final product fragments. The movement of protons can occur either directly from the z- to c-fragment or in a more complex manner including a ping-pong-type mechanism. The nature of these diverse hydrogen-bonding motifs reveals that not only those functional groups proximate to the bond rupture site, but also the entire global chemical environment, play important roles in backbone cleavage characteristic of ECD/ETD MS/MS. For doubly charged systems, both conformation and electron localization site dictate which of the two fragments retains the final positive charge.
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Affiliation(s)
- Konstantin O Zhurov
- Biomolecular Mass Spectrometry Laboratory and ‡Laboratory for Computational Molecular Design, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
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13
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Pepin R, Laszlo KJ, Peng B, Marek A, Bush MF, Tureček F. Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer: From Electron Attachment to Backbone Cleavage, Ion–Molecule Complexes, and Fragment Separation. J Phys Chem A 2013; 118:308-24. [DOI: 10.1021/jp411100c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Robert Pepin
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Kenneth J. Laszlo
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Bo Peng
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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14
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Le TN, Poully JC, Lecomte F, Nieuwjaer N, Manil B, Desfrançois C, Chirot F, Lemoine J, Dugourd P, van der Rest G, Grégoire G. Gas-phase structure of amyloid-β (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1937-49. [PMID: 24043520 DOI: 10.1007/s13361-013-0722-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/22/2013] [Accepted: 07/30/2013] [Indexed: 05/11/2023]
Abstract
The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.
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Affiliation(s)
- Thi Nga Le
- Université Paris 13, Sorbonne Paris Cité, Laboratoire de Physique des Lasers, CNRS UMR 7538, F-93430, Villetaneuse, France
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15
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Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
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16
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Zhurov KO, Fornelli L, Wodrich MD, Laskay ÜA, Tsybin YO. Principles of electron capture and transfer dissociation mass spectrometry applied to peptide and protein structure analysis. Chem Soc Rev 2013; 42:5014-30. [DOI: 10.1039/c3cs35477f] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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17
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Kalli A, Hess S. Electron capture dissociation of hydrogen-deficient peptide radical cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1729-1740. [PMID: 22855421 DOI: 10.1007/s13361-012-0433-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/05/2012] [Accepted: 06/12/2012] [Indexed: 06/01/2023]
Abstract
Hydrogen-deficient peptide radical cations exhibit fascinating gas phase chemistry, which is governed by radical driven dissociation and, in many cases, by a combination of radical and charge driven fragmentation. Here we examine electron capture dissociation (ECD) of doubly, [M + H](2+•), and triply, [M + 2H](3+•), charged hydrogen-deficient species, aiming to investigate the effect of a hydrogen-deficient radical site on the ECD outcome and characterize the dissociation pathways of hydrogen-deficient species in ECD. ECD of [M + H](2+•) and [M + 2H](3+•) precursor ions resulted in efficient electron capture by the hydrogen-deficient species. However, the intensities of c- and z-type product ions were reduced, compared with those observed for the even electron species, indicating suppression of N-C(α) backbone bond cleavages. We postulate that radical recombination occurs after the initial electron capture event leading to a stable even electron intermediate, which does not trigger N-C(α) bond dissociations. Although the intensities of c- and z-type product ions were reduced, the number of backbone bond cleavages remained largely unaffected between the ECD spectra of the even electron and hydrogen-deficient species. We hypothesize that a small ion population exist as a biradical, which can trigger N-C(α) bond cleavages. Alternatively, radical recombination and N-C(α) bond cleavages can be in competition, with radical recombination being the dominant pathway and N-C(α) cleavages occurring to a lesser degree. Formation of b- and y-type ions observed for two of the hydrogen-deficient peptides examined is also discussed.
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Affiliation(s)
- Anastasia Kalli
- Proteome Exploration Laboratory, Division of Biology, Beckman Institute, California Institute of Technology, Pasadena, 91125, USA
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18
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Zimnicka M, Chung TW, Moss CL, Tureček F. Perturbing Peptide Cation-Radical Electronic States by Thioxoamide Groups: Formation, Dissociations, and Energetics of Thioxopeptide Cation-Radicals. J Phys Chem A 2012; 117:1265-75. [DOI: 10.1021/jp305865q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Magdalena Zimnicka
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle,
Washington 98195-1700,
United States
| | - Thomas W. Chung
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle,
Washington 98195-1700,
United States
| | - Christopher L. Moss
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle,
Washington 98195-1700,
United States
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle,
Washington 98195-1700,
United States
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19
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Pérot-Taillandier M, Zirah S, Rebuffat S, Linne U, Marahiel MA, Cole RB, Tabet JC, Afonso C. Determination of Peptide Topology through Time-Resolved Double-Resonance under Electron Capture Dissociation Conditions. Anal Chem 2012; 84:4957-64. [DOI: 10.1021/ac300607y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Moss CL, Liang W, Li X, Tureček F. The early life of a peptide cation-radical. Ground and excited-state trajectories of electron-based peptide dissociations during the first 330 femtoseconds. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:446-459. [PMID: 22187160 DOI: 10.1007/s13361-011-0283-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 10/11/2011] [Accepted: 10/18/2011] [Indexed: 05/31/2023]
Abstract
We report a new approach to investigating the mechanisms of fast peptide cation-radical dissociations based on an analysis of time-resolved reaction progress by Ehrenfest dynamics, as applied to an Ala-Arg cation-radical model system. Calculations of stationary points on the ground electronic state that were carried out with effective CCSD(T)/6-311++G(3df,2p) could not explain the experimental branching ratios for loss of a hydrogen atom, ammonia, and N-C(α) bond dissociation in (AR + 2H)(+•). The Ehrenfest dynamics results indicate that the ground and low-lying excited electronic states of (AR + 2H)(+•) follow different reaction courses in the first 330 femtoseconds after electron attachment. The ground (X) state undergoes competing loss of N-terminal ammonia and isomerization to an aminoketyl radical intermediate that depend on the vibrational energy of the charge-reduced ion. The A and B excited states involve electron capture in the Arg guanidine and carboxyl groups and are non-reactive on the short time scale. The C state is dissociative and progresses to a fast loss of an H atom from the Arg guanidine group. Analogous results were obtained by using the B3LYP and CAM-B3LYP density functionals for the excited state dynamics and including the universal M06-2X functional for ground electronic state calculations. The results of this Ehrenfest dynamics study indicate that reaction pathway branching into the various dissociation channels occurs in the early stages of electron attachment and is primarily determined by the electronic states being accessed. This represents a new paradigm for the discussion of peptide dissociations in electron based methods of mass spectrometry.
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Affiliation(s)
- Christopher L Moss
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, USA
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21
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Fragmentation methods on the balance: unambiguous top–down mass spectrometric characterization of oxaliplatin–ubiquitin binding sites. Anal Bioanal Chem 2011; 402:2655-62. [DOI: 10.1007/s00216-011-5523-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/19/2011] [Accepted: 10/19/2011] [Indexed: 10/15/2022]
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22
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Tsybin YO, Fornelli L, Stoermer C, Luebeck M, Parra J, Nallet S, Wurm FM, Hartmer R. Structural Analysis of Intact Monoclonal Antibodies by Electron Transfer Dissociation Mass Spectrometry. Anal Chem 2011; 83:8919-27. [DOI: 10.1021/ac201293m] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yury O. Tsybin
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Luca Fornelli
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | | | - Julien Parra
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Sophie Nallet
- Cellular Biotechnology Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Florian M. Wurm
- Cellular Biotechnology Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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23
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Yoo HJ, Wang N, Zhuang S, Song H, Håkansson K. Negative-Ion Electron Capture Dissociation: Radical-Driven Fragmentation of Charge-Increased Gaseous Peptide Anions. J Am Chem Soc 2011; 133:16790-3. [DOI: 10.1021/ja207736y] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Hyun Ju Yoo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Ning Wang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Shuyi Zhuang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Hangtian Song
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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24
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Roy S, Davydova MP, Pal R, Gilmore K, Tolstikov GA, Vasilevsky SF, Alabugin IV. Dissecting Alkynes: Full Cleavage of Polarized C≡C Moiety via Sequential Bis-Michael Addition/Retro-Mannich Cascade. J Org Chem 2011; 76:7482-90. [DOI: 10.1021/jo201259j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saumya Roy
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | | | - Runa Pal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Kerry Gilmore
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | | | | | - Igor V. Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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25
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Albrieux F, Hamidane HB, Calvo F, Chirot F, Tsybin YO, Antoine R, Lemoine J, Dugourd P. Structural Preferences of Gas-Phase M2TMP Monomers upon Sequence Variations. J Phys Chem A 2011; 115:4711-8. [DOI: 10.1021/jp110732h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Hisham Ben Hamidane
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | | | - Yury O. Tsybin
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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26
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Moss CL, Chung TW, Čeřovský V, Tureček F. Electron transfer dissociation of a melectin peptide: correlating the precursor ion structure with peptide backbone dissociations. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Electron transfer dissociation (ETD) of doubly and triply charged ions from the amphipathic N-terminal decapeptide GFLSILKKVL-NH2 segment of melectin gave different distributions of fragment ions. The triply charged ions generated extensive series of fragment ions of c and z type that covered the entire sequence from both the N and C termini. In contrast, electron transfer to the doubly charged ions caused backbone cleavages that occurred at residues close to the N and C termini. Attachment of a free low-energy electron to the doubly charged ions caused primary dissociations close to the N and C termini that were followed by consecutive dissociations of z ions. The structure of gaseous doubly charged ions from the melectin peptide was elucidated by a combination of exhaustive conformational search by force-field molecular dynamics, large-scale gradient optimization using the semiempirical PM6 method, and density functional theory single-point energy and gradient optimization calculations. The most stable doubly charged ions were found to be protonated at the lysine ε-amino groups and have globular conformations. The backbone cleavages in ETD correlated with the electronic structure of cation-radicals produced by electron attachment to the most stable conformers. The charged lysine ammonium groups direct the incoming electron to the π* orbitals at the proximate amide groups at Phe, Leu, Lys and Val residues that show the highest spin densities. Electron attachment at these amide groups weakens the N–Cα bonds between the Phe-Leu, Leu-Ser, Lys-Lys and Lys-Val residues and causes backbone dissociations.
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27
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Sargaeva NP, Lin C, O’Connor PB. Unusual fragmentation of β-linked peptides by ExD tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:480-91. [PMID: 21472566 PMCID: PMC4361814 DOI: 10.1007/s13361-010-0049-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 11/18/2010] [Accepted: 11/18/2010] [Indexed: 05/11/2023]
Abstract
Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) represent a powerful tool for biological analysis. ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β(3)-type amino acid that has an additional methylene group in the backbone, forming a C(α)-C(β) bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a C(α)-C(β) bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N-C(β) and C(α)-C(β) bond cleavages were rare, providing few c and z• type fragments, which was attributed to the instability of the C(β) radical. Instead, the electron capture resulted primarily in the formation of a• and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the β amino acid residues.
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Affiliation(s)
- Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
- To whom correspondence should be addressed: Phone: +44 (0)2476 151 008, Fax: +44 (0)2476 151 009,
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28
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Ben Hamidane H, Vorobyev A, Tsybin YO. Repeatability and reproducibility of product ion abundances in electron capture dissociation mass spectrometry of peptides. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2011; 17:321-331. [PMID: 22006634 DOI: 10.1255/ejms.1143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Site-specific reproducibility and repeatability of electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) are of fundamental importance for product ion abundance (PIA)-based peptide and protein structure analysis. However, despite the growing interest in ECD PIA-based applications, these parameters have not yet been investigated in a consistent manner. Here, we first provide a detailed description of the experimental parameters for ECD-based tandem mass spectrometry performed on a hybrid linear ion trap (LTQ) FT-ICR MS. In the following, we describe the evaluation and comparison of ECD and infrared multiphoton dissociation (IRMPD) PIA methodologies upon variation of a number of experimental parameters, for example, cathode potential (electron energy), laser power, electron and photon irradiation periods and pre- irradiation delays, as well as precursor ion number. Ranges of experimental parameters that yielded an average PIA variation below 5% and 15% were determined for ECD and IRMPD, respectively. We report cleavage site-dependent ECD PIA variation below 20% and correlation coefficients between fragmentation patterns superior to 0.95 for experiments performed on three FT-ICR MS instruments. Overall, the encouraging results obtained for ECD PIA reproducibility and repeatability support the use of ECD PIA as a complementary source of information to m/z data in radical-induced dissociation applied for peptide and protein structure analysis.
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29
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Nishikaze T, Takayama M. Influence of charge state and amino acid composition on hydrogen transfer in electron capture dissociation of peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1979-1988. [PMID: 20869879 DOI: 10.1016/j.jasms.2010.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/09/2010] [Accepted: 08/15/2010] [Indexed: 05/29/2023]
Abstract
Although conventional N-Cα bond cleavage in electron capture dissociation (ECD) of multiply-charged peptides generates a complementary c' and z(·) fragment pair, the N-Cα cleavage followed by hydrogen transfer from c' to z(·) fragments produces other fragments, namely c(·) and z'. In this study, the influence of charge state and amino acid composition on hydrogen transfer in ECD is described using sets of peptides. Hydrogen transferred ionic species such as c(·) and z' were observed in ECD spectra of doubly-protonated peptides, while the triply-protonated form did not demonstrate hydrogen transfer. The extent of hydrogen transfer in ECD of doubly-protonated peptides was dependent on constituent amino acids. The ECD of doubly-protonated peptides possessing numerous basic sites showed extensive hydrogen transfer compared with ECD of less basic peptides. The extent of hydrogen transfer is discussed from the viewpoints of the structure of peptide ions, the possibility of internal hydrogen bonding and intermediate lifetime of complex [c' + z(·)].
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Affiliation(s)
- Takashi Nishikaze
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan.
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30
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Turecek F, Chung TW, Moss CL, Wyer JA, Ehlerding A, Holm AIS, Zettergren H, Nielsen SB, Hvelplund P, Chamot-Rooke J, Bythell B, Paizs B. The histidine effect. Electron transfer and capture cause different dissociations and rearrangements of histidine peptide cation-radicals. J Am Chem Soc 2010; 132:10728-40. [PMID: 20681705 DOI: 10.1021/ja907808h] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron-transfer and -capture dissociations of doubly protonated peptides gave dramatically different product ions for a series of histidine-containing pentapeptides of both non-tryptic (AAHAL, AHAAL, AHADL, AHDAL) and tryptic (AAAHK, AAHAK, AHAAK, HAAAK, AAAHR, AAHAR, AHAAR, HAAAR) type. Electron transfer from gaseous Cs atoms and fluoranthene anions triggered backbone dissociations of all four N-C(alpha) bonds in the peptide ions in addition to loss of H and NH(3). Substantial fractions of charge-reduced cation-radicals did not dissociate on an experimental time scale ranging from 10(-6) to 10(-1) s. Multistage tandem mass spectrometric (MS(n)) experiments indicated that the non-dissociating cation-radicals had undergone rearrangements. These were explained as being due to proton migrations from N-terminal ammonium and COOH groups to the C-2' position of the reduced His ring, resulting in substantial radical stabilization. Ab initio calculations revealed that the charge-reduced cation-radicals can exist as low-energy zwitterionic amide pi* states which were local energy minima. These states underwent facile exothermic proton migrations to form aminoketyl radical intermediates, whereas direct N-C(alpha) bond cleavage in zwitterions was disfavored. RRKM analysis indicated that backbone N-C(alpha) bond cleavages did not occur competitively from a single charge-reduced precursor. Rather, these bond cleavages proceeded from distinct intermediates which originated from different electronic states accessed by electron transfer. In stark contrast to electron transfer, capture of a free electron by the peptide ions mainly induced radical dissociations of the charge-carrying side chains and loss of a hydrogen atom followed by standard backbone dissociations of even-electron ions. The differences in dissociation are explained by different electronic states being accessed upon electron transfer and capture.
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Affiliation(s)
- Frantisek Turecek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, USA.
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31
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Breuker K, Brüschweiler S, Tollinger M. Electrostatic Stabilization of a Native Protein Structure in the Gas Phase. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Breuker K, Brüschweiler S, Tollinger M. Electrostatic stabilization of a native protein structure in the gas phase. Angew Chem Int Ed Engl 2010; 50:873-7. [PMID: 21246681 PMCID: PMC3045662 DOI: 10.1002/anie.201005112] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Indexed: 11/17/2022]
Affiliation(s)
- Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck, Universität Innsbruck, Innrain 52a, 6020 Innsbruck, Austria.
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33
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Zhang Z. Prediction of electron-transfer/capture dissociation spectra of peptides. Anal Chem 2010; 82:1990-2005. [PMID: 20148580 DOI: 10.1021/ac902733z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An empirical model, based on classic kinetics, was developed for quantitative prediction of electron-transfer dissociation (ETD) and electron-capture dissociation (ECD) spectra of peptides. The model includes most fragmentation pathways described in the literature plus some additional pathways based on the author's assumptions and observations. The ETD model was trained with more than 7000 ETD spectra, with and without supplemental activation. The ECD model was trained with more than 6000 ECD spectra. The trained ETD and ECD models are able to predict ETD and ECD spectra with reasonable accuracy in ion intensities for peptide precursors up to 4000 u in mass.
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Affiliation(s)
- Zhongqi Zhang
- Process and Product Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, USA.
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34
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Larraillet V, Vorobyev A, Brunet C, Lemoine J, Tsybin YO, Antoine R, Dugourd P. Comparative dissociation of peptide polyanions by electron impact and photo-induced electron detachment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:670-680. [PMID: 20171119 DOI: 10.1016/j.jasms.2010.01.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/11/2010] [Accepted: 01/14/2010] [Indexed: 05/28/2023]
Abstract
We compare product-ion mass spectra produced by electron detachment dissociation (EDD) and electron photodetachment dissociation (EPD) of multi-deprotonated peptides on a Fourier transform and a linear ion trap mass spectrometer, respectively. Both methods, EDD and EPD, involve the electron emission-induced formation of a radical oxidized species from a multi-deprotonated precursor peptide. Product-ion mass spectra display mainly fragment ions resulting from backbone cleavages of C(alpha)-C bond ruptures yielding a and x ions. Fragment ions originating from N-C(alpha) backbone bond cleavages are also observed, in particular by EPD. Although EDD and EPD methods involve the generation of a charge-reduced radical anion intermediate by electron emission, the product ion abundance distributions are drastically different. Both processes seem to be triggered by the location and the recombination of radicals (both neutral and cation radicals). Therefore, EPD product ions are predominantly formed near tryptophan and histidine residues, whereas in EDD the negative charge solvation sites on the backbone seem to be the most favorable for the nearby bond dissociation.
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35
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Jones AW, Mikhailov VA, Iniesta J, Cooper HJ. Electron capture dissociation mass spectrometry of tyrosine nitrated peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:268-277. [PMID: 19931467 DOI: 10.1016/j.jasms.2009.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 09/08/2009] [Accepted: 10/14/2009] [Indexed: 05/28/2023]
Abstract
In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification. Here, we have investigated the electron capture dissociation (ECD) and collision-induced dissociation (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains.
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Affiliation(s)
- Andrew W Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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Vasicek L, Brodbelt JS. Enhanced electron transfer dissociation through fixed charge derivatization of cysteines. Anal Chem 2009; 81:7876-84. [PMID: 19722535 DOI: 10.1021/ac901482s] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron transfer dissociation (ETD) has proven to be a promising new ion activation method for proteomics applications due to its ability to generate c- and z-type fragment ions in comparison to the y- and b-type ions produced upon the more conventional collisional activation of peptides. However, low precursor charge states hinder the success of electron-based activation methods due to competition from nondissociative charge reduction and incomplete sequence coverage. In the present report, the reduction and alkylation of disulfide bonds prior to ETD analysis is evaluated by comparison of three derivatization reagents: iodoacetamide (IAM), N,N-dimethyl-2-chloro-ethylamine (DML), and (3-acrylamidopropyl)-trimethyl ammonium chloride (APTA). While both the DML and APTA modifications lead to an increase in the charge states of peptides, the APTA-peptides provided the most significant improvement in percent fragmentation and sequence coverage for all peptides upon ETD, including formation of diagnostic ions that allow characterization of both the C- and N-termini. In addition, the formation of product ions in multiple charge states upon ETD is minimized for the APTA-modified peptides.
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Affiliation(s)
- Lisa Vasicek
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
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Vorobyev A, Ben Hamidane H, Tsybin YO. Electron capture dissociation product ion abundances at the X amino acid in RAAAA-X-AAAAK peptides correlate with amino acid polarity and radical stability. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:2273-2283. [PMID: 19811930 DOI: 10.1016/j.jasms.2009.08.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 08/22/2009] [Accepted: 08/23/2009] [Indexed: 05/28/2023]
Abstract
We present mechanistic studies aimed at improving the understanding of the product ion formation rules in electron capture dissociation (ECD) of peptides and proteins in Fourier transform ion cyclotron resonance mass spectrometry. In particular, we attempted to quantify the recently reported general correlation of ECD product ion abundance (PIA) with amino acid hydrophobicity. The results obtained on a series of model H-RAAAAXAAAAK-OH peptides confirm a direct correlation of ECD PIA with X amino acid hydrophobicity and polarity. The correlation factor (R) exceeds 0.9 for 12 amino acids (Ile, Val, His, Asn, Asp, Glu, Gln, Ser, Thr, Gly, Cys, and Ala). The deviation of ECD PIA for seven outliers (Pro is not taken into consideration) is explained by their specific radical stabilization properties (Phe, Trp, Tyr, Met, and Leu) and amino acid basicity (Lys, Arg). Phosphorylation of Ser, Thr, and Tyr decreases the efficiency of ECD around phosphorylated residues, as expected. The systematic arrangement of amino acids reported here indicates a possible route toward development of a predictive model for quantitative electron capture/transfer dissociation tandem mass spectrometry, with possible applications in proteomics.
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Affiliation(s)
- Aleksey Vorobyev
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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