1
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Paris J, Theisen A, Marzullo BP, Haris A, Morgan TE, Barrow MP, O’Hara J, O’Connor PB. Multimodal Tandem Mass Spectrometry Techniques for the Analysis of Phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1126-1133. [PMID: 35604791 PMCID: PMC9264387 DOI: 10.1021/jasms.1c00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), ultraviolet photodissociation (UVPD), electron capture dissociation and electron detachment dissociation (EDD) experiments were conducted on a set of phosphopeptides, in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation patterns were compared and varied according to the fragmentation mechanisms and the composition of the peptides. CAD and IRMPD produced similar fragmentation profiles of the phosphopeptides, while UVPD produced a large number of complementary fragments. Electron-based dissociation techniques displayed lower fragmentation efficiencies, despite retaining the labile phosphate group, and drastically different fragmentation profiles. EDD produced complex spectra whose interpretation proved challenging.
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Affiliation(s)
- Johanna Paris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alina Theisen
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bryan P. Marzullo
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Anisha Haris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tomos E. Morgan
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark P. Barrow
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - John O’Hara
- UCB, 216 Bath Road, Slough SL1 3WE, United
Kingdom
| | - Peter B. O’Connor
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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2
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Jeanne Dit Fouque K, Wellmann M, Leyva Bombuse D, Santos-Fernandez M, Cintron-Diaz YL, Gomez-Hernandez ME, Kaplan D, Voinov VG, Fernandez-Lima F. Effective discrimination of gas-phase peptide conformers using TIMS-ECD-ToF MS/MS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5216-5223. [PMID: 34698320 PMCID: PMC8596503 DOI: 10.1039/d1ay01461g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In the present work, four, well-studied, model peptides (e.g., substance P, bradykinin, angiotensin I and AT-Hook 3) were used to correlate structural information provided by ion mobility and ECD/CID fragmentation in a TIMS-q-EMS-ToF MS/MS platform, incorporporating an electromagnetostatic cell (EMS). The structural heterogeneity of the model peptides was observed by (i) multi-component ion mobility profiles (high ion mobility resolving power, R ∼115-145), and (ii) fast online characteristic ECD fragmentation patterns per ion mobility band (∼0.2 min). Particularly, it was demonstrated that all investigated species were probably conformers, involving cis/trans-isomerizations at X-Pro peptide bond, following the same protonation schemes, in good agreement with previous ion mobility and single point mutation experiments. The comparison between ion mobility selected ECD spectra and traditional FT-ICR ECD MS/MS spectra showed comparable ECD fragmentation efficiencies but differences in the ratio of radical (˙)/prime (') fragment species (H˙ transfer), which were associated with the differences in detection time after the electron capture event. The analysis of model peptides using online TIMS-q-EMSToF MS/MS provided complementary structural information on the intramolecular interactions that stabilize the different gas-phase conformations to those obtained by ion mobility or ECD alone.
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Affiliation(s)
- K Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
| | - M Wellmann
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Kiel 24098, Germany
| | - D Leyva Bombuse
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - M Santos-Fernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Y L Cintron-Diaz
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - M E Gomez-Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - D Kaplan
- KapScience LLC, Tewksbury, MA 01876, USA
| | - V G Voinov
- e-MSion Inc., Corvallis, OR 97330, USA
- Linus Pauling Institute and Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - F Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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3
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Lermyte F, Everett J, Lam YPY, Wootton CA, Brooks J, Barrow MP, Telling ND, Sadler PJ, O'Connor PB, Collingwood JF. Metal Ion Binding to the Amyloid β Monomer Studied by Native Top-Down FTICR Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2123-2134. [PMID: 31350722 PMCID: PMC6805827 DOI: 10.1007/s13361-019-02283-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
Native top-down mass spectrometry is a fast, robust biophysical technique that can provide molecular-scale information on the interaction between proteins or peptides and ligands, including metal cations. Here we have analyzed complexes of the full-length amyloid β (1-42) monomer with a range of (patho)physiologically relevant metal cations using native Fourier transform ion cyclotron resonance mass spectrometry and three different fragmentation methods-collision-induced dissociation, electron capture dissociation, and infrared multiphoton dissociation-all yielding consistent results. Amyloid β is of particular interest as its oligomerization and aggregation are major events in the etiology of Alzheimer's disease, and it is known that interactions between the peptide and bioavailable metal cations have the potential to significantly damage neurons. Those metals which exhibited the strongest binding to the peptide (Cu2+, Co2+, Ni2+) all shared a very similar binding region containing two of the histidine residues near the N-terminus (His6, His13). Notably, Fe3+ bound to the peptide only when stabilized toward hydrolysis, aggregation, and precipitation by a chelating ligand, binding in the region between Ser8 and Gly25. We also identified two additional binding regions near the flexible, hydrophobic C-terminus, where other metals (Mg2+, Ca2+, Mn2+, Na+, and K+) bound more weakly-one centered on Leu34, and one on Gly38. Unexpectedly, collisional activation of the complex formed between the peptide and [CoIII(NH3)6]3+ induced gas-phase reduction of the metal to CoII, allowing the peptide to fragment via radical-based dissociation pathways. This work demonstrates how native mass spectrometry can provide new insights into the interactions between amyloid β and metal cations.
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Affiliation(s)
- Frederik Lermyte
- School of Engineering, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - James Everett
- School of Engineering, University of Warwick, Coventry, CV4 7AL, UK
- Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Yuko P Y Lam
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Jake Brooks
- School of Engineering, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Neil D Telling
- Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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4
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Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv 2018; 9:313-344. [PMID: 35521579 PMCID: PMC9059502 DOI: 10.1039/c8ra07200k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022] Open
Abstract
Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.
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Affiliation(s)
- P Boomathi Pandeswari
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
| | - Varatharajan Sabareesh
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
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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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Schneeberger EM, Breuker K. Replacing H + by Na + or K + in phosphopeptide anions and cations prevents electron capture dissociation. Chem Sci 2018; 9:7338-7353. [PMID: 30542537 PMCID: PMC6237128 DOI: 10.1039/c8sc02470g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/07/2018] [Indexed: 01/29/2023] Open
Abstract
By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.
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Affiliation(s)
- Eva-Maria Schneeberger
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| | - Kathrin Breuker
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
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7
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Giuliani A, Williams JP, Green MR. Extreme Ultraviolet Radiation: A Means of Ion Activation for Tandem Mass Spectrometry. Anal Chem 2018; 90:7176-7180. [DOI: 10.1021/acs.analchem.8b01789] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandre Giuliani
- Synchrotron SOLEIL, L’Orme des Merisiers, Gif-sur-Yvette F-91190, France
- UAR 1008 CEPIA, INRA, Nantes F-44316, France
| | | | - Martin R. Green
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, U.K
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8
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Tang Y, Pu Y, Gao J, Hong P, Costello CE, Lin C. De Novo Glycan Sequencing by Electronic Excitation Dissociation and Fixed-Charge Derivatization. Anal Chem 2018; 90:3793-3801. [PMID: 29443510 DOI: 10.1021/acs.analchem.7b04077] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Detailed glycan structural characterization is frequently achieved by collisionally activated dissociation (CAD) based sequential tandem mass spectrometry (MS n) analysis of permethylated glycans. However, it is challenging to implement MS n ( n > 2) during online glycan separation, and this has limited its application to analysis of complex glycan mixtures from biological samples. Further, permethylation can reduce liquid chromatographic (LC) resolution of isomeric glycans. Here, we studied the electronic excitation dissociation (EED) fragmentation behavior of native glycans with a reducing-end fixed charge tag and identified key spectral features that are useful for topology and linkage determination. We also developed a de novo glycan sequencing software that showed remarkable accuracy in glycan topology elucidation based on the EED spectra of fixed charge-derivatized glycans. The ability to obtain glycan structural details at the MS2 level, without permethylation, via a combination of fixed charge derivatization, EED, and de novo spectral interpretation, makes the present approach a promising tool for comprehensive and rapid characterization of glycan mixtures.
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Affiliation(s)
- Yang Tang
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Yi Pu
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Jinshan Gao
- Department of Chemistry and Biochemistry , Montclair State University , Montclair , New Jersey 07043 , United States
| | - Pengyu Hong
- Department of Computer Science, Brandeis University , Waltham , Massachusetts 02453 , United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
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9
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van Agthoven MA, Lynch AM, Morgan TE, Wootton CA, Lam YPY, Chiron L, Barrow MP, Delsuc MA, O'Connor PB. Can Two-Dimensional IR-ECD Mass Spectrometry Improve Peptide de Novo Sequencing? Anal Chem 2018; 90:3496-3504. [PMID: 29420878 DOI: 10.1021/acs.analchem.7b05324] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two-dimensional mass spectrometry (2D MS) correlates precursor and fragment ions without ion isolation in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) for tandem mass spectrometry. Infrared activated electron capture dissociation (IR-ECD), using a hollow cathode configuration, generally yields more information for peptide sequencing in tandem mass spectrometry than ECD (electron capture dissociation) alone. The effects of the fragmentation zone on the 2D mass spectrum are investigated as well as the structural information that can be derived from it. The enhanced structural information gathered from the 2D mass spectrum is discussed in terms of how de novo peptide sequencing can be performed with increased confidence. 2D IR-ECD MS is shown to sequence peptides, to distinguish between leucine and isoleucine residues through the production of w ions as well as between C-terminal ( b/ c) and N-terminal ( y/ z) fragments through the use of higher harmonics, and to assign and locate peptide modifications.
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Affiliation(s)
- Maria A van Agthoven
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Alice M Lynch
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Tomos E Morgan
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Christopher A Wootton
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Yuko P Y Lam
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Lionel Chiron
- CASC4DE, Le Lodge , 20 av. du Neuhof , 67100 Strasbourg , France
| | - Mark P Barrow
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Marc-André Delsuc
- CASC4DE, Le Lodge , 20 av. du Neuhof , 67100 Strasbourg , France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U596; CNRS, UMR7104 , Université de Strasbourg , 1 rue Laurent Fries , 67404 Illkirch-Graffenstaden , France
| | - Peter B O'Connor
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
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10
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Jeanne Dit Fouque K, Lavanant H, Zirah S, Hegemann JD, Fage CD, Marahiel MA, Rebuffat S, Afonso C. General rules of fragmentation evidencing lasso structures in CID and ETD. Analyst 2018; 143:1157-1170. [DOI: 10.1039/c7an02052j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked structure in which the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring.
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Affiliation(s)
| | | | - S. Zirah
- Muséum National d'Histoire Naturelle
- Sorbonne Universités
- Centre national de la Recherche scientifique
- Laboratoire Molécules de Communication et Adaptation des Microorganismes
- UMR 7245 CNRS-MNHN
| | - J. D. Hegemann
- Roger Adams Laboratory
- Department of Chemistry
- University of Illinois at Urbana–Champaign
- Urbana
- USA
| | - C. D. Fage
- Department of Chemistry
- Biochemistry; LOEWE Center for Synthetic Microbiology
- Philipps-University Marburg
- Marburg
- Germany
| | - M. A. Marahiel
- Department of Chemistry
- Biochemistry; LOEWE Center for Synthetic Microbiology
- Philipps-University Marburg
- Marburg
- Germany
| | - S. Rebuffat
- Muséum National d'Histoire Naturelle
- Sorbonne Universités
- Centre national de la Recherche scientifique
- Laboratoire Molécules de Communication et Adaptation des Microorganismes
- UMR 7245 CNRS-MNHN
| | - C. Afonso
- Normandie Univ
- UNIROUEN
- INSA Rouen
- CNRS
- COBRA
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11
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Qi Y, Volmer DA. Electron-based fragmentation methods in mass spectrometry: An overview. MASS SPECTROMETRY REVIEWS 2017; 36:4-15. [PMID: 26445267 DOI: 10.1002/mas.21482] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/03/2015] [Accepted: 07/03/2015] [Indexed: 05/21/2023]
Abstract
Tandem mass spectrometry (MS/MS) provides detailed information for structural characterization of biomolecules. The combination of electron capture dissociation (ECD) techniques with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) often provides unique ion-electron reactions and fragmentation channels in MS/MS. ECD is often a complimentary, sometimes even a superior tool to conventional MS/MS techniques. This article is aimed at providing a short overview of ECD-based fragmentation techniques (ExD) and optimization of ECD experiments for FTICR mass analyzers. Most importantly, it is meant to pique the interest of potential users for this exciting research field. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:4-15, 2017.
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Affiliation(s)
- Yulin Qi
- Institute of Bioanalytical Chemistry, Saarland University, Campus B2.2, Saarbrücken, 66123, Germany
| | - Dietrich A Volmer
- Institute of Bioanalytical Chemistry, Saarland University, Campus B2.2, Saarbrücken, 66123, Germany
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12
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Fagerquist CK. Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization. Expert Rev Proteomics 2016; 14:97-107. [DOI: 10.1080/14789450.2017.1260451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clifton K. Fagerquist
- United States Department of Agriculture (USDA), Agricultural Research Service, Albany, CA, USA
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13
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Schennach M, Schneeberger EM, Breuker K. Unfolding and Folding of the Three-Helix Bundle Protein KIX in the Absence of Solvent. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1079-88. [PMID: 26936183 PMCID: PMC4863917 DOI: 10.1007/s13361-016-1363-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation was used to probe the structure, unfolding, and folding of KIX ions in the gas phase. At energies for vibrational activation that were sufficiently high to cause loss of small molecules such as NH3 and H2O by breaking of covalent bonds in about 5% of the KIX (M + nH)(n+) ions with n = 7-9, only partial unfolding was observed, consistent with our previous hypothesis that salt bridges play an important role in stabilizing the native solution fold after transfer into the gas phase. Folding of the partially unfolded ions on a timescale of up to 10 s was observed only for (M + nH)(n+) ions with n = 9, but not n = 7 and n = 8, which we attribute to differences in the distribution of charges within the (M + nH)(n+) ions. Graphical Abstract ᅟ.
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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
| | - Eva-Maria Schneeberger
- 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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14
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Takahashi H, Sekiya S, Nishikaze T, Kodera K, Iwamoto S, Wada M, Tanaka K. Hydrogen Attachment/Abstraction Dissociation (HAD) of Gas-Phase Peptide Ions for Tandem Mass Spectrometry. Anal Chem 2016; 88:3810-6. [DOI: 10.1021/acs.analchem.5b04888] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hidenori Takahashi
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Sadanori Sekiya
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Takashi Nishikaze
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Kei Kodera
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Motoi Wada
- Graduate
School of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Koichi Tanaka
- Koichi Tanaka
Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
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15
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Wongkongkathep P, Li H, Zhang X, Loo RRO, Julian RR, Loo JA. Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:137-145. [PMID: 26644781 PMCID: PMC4669582 DOI: 10.1016/j.ijms.2015.07.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in combination with ECD allowed the three disulfide bonds of insulin to be cleaved and the overall sequence coverage to be increased. For the larger sized ribonuclease A with four disulfide bonds, irradiation from an infrared laser (10.6 µm) to disrupt non-covalent interactions was combined with UV-activation to facilitate the cleavage of up to three disulfide bonds. Preferences for disulfide bond cleavage are dependent on protein structure and sequence. Disulfide bonds can reform if the generated radicals remain in close proximity. By varying the time delay between the UV-activation and the ECD events, it was determined that disulfide bonds reform within 10-100 msec after their UV-homolytic cleavage.
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Affiliation(s)
- Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Huilin Li
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Xing Zhang
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521
| | - Rachel R. Ogorzalek Loo
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Ryan R. Julian
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles Los Angeles, CA 90095
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
- UCLA/DOE Institute of Genomics and Proteomics, University of California-Los Angeles Los Angeles, CA 90095
- Corresponding author at: University of California-Los Angeles, Department of Chemistry and Biochemistry, 402 Boyer Hall, Molecular Biology Institute, Los Angeles, CA, United States, Tel.: +1 310 794 7023; fax: +1 310 206 4038, (J.A. Loo)
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16
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Characterization of top-down ETD in a travelling-wave ion guide. Methods 2015; 89:22-9. [DOI: 10.1016/j.ymeth.2015.05.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/30/2015] [Accepted: 05/19/2015] [Indexed: 11/20/2022] Open
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17
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Baba T, Campbell JL. Capturing Polyradical Protein Cations after an Electron Capture Event: Evidence for their Stable Distonic Structures in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1695-1701. [PMID: 26231348 DOI: 10.1007/s13361-015-1207-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
We report on the formation and "capture" of polyradical protein cations after an electron capture event. Performed in a unique electron-capture dissociation (ECD) instrument, these experiments can generate reduced forms of multiply protonated proteins by sequential charge reduction using electrons with ~1 eV. The true structures of these possible polyradicals is considered: Do the introduced unpaired electrons recombine quickly to form a new two-electron bond, or do these unpaired electrons exist as radical sites with appropriate chemical reactivity? Using an established chemical probe--radical quenching with molecular oxygen--we demonstrate that these charge-reduced protein cations are indeed polyradicals that form adducts with up to three molecules of oxygen (i.e., tri-radical protein cations) that are stable for at least 100 ms.
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Affiliation(s)
- Takashi Baba
- Sciex, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada.
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18
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Lermyte F, Sobott F. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes. Proteomics 2015; 15:2813-22. [DOI: 10.1002/pmic.201400516] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/13/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Frederik Lermyte
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
| | - Frank Sobott
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
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19
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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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20
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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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21
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Li H, Snelling JR, Barrow MP, Scrivens JH, Sadler PJ, O'Connor PB. Mass spectrometric strategies to improve the identification of Pt(II)-modification sites on peptides and proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1217-27. [PMID: 24845349 DOI: 10.1007/s13361-014-0877-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 01/17/2014] [Accepted: 02/23/2014] [Indexed: 05/22/2023]
Abstract
To further explore the binding chemistry of cisplatin (cis-Pt(NH3)2Cl2) to peptides and also establish mass spectrometry (MS) strategies to quickly assign the platinum-binding sites, a series of peptides with potential cisplatin binding sites (Met(S), His(N), Cys(S), disulfide, carboxyl groups of Asp and Glu, and amine groups of Arg and Lys, were reacted with cisplatin, then analyzed by electron capture dissociation (ECD) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Radical-mediated side-chain losses from the charge-reduced Pt-binding species (such as CH3S(•) or CH3SH from Met, SH(•) from Cys, CO2 from Glu or Asp, and NH2(•) from amine groups) were found to be characteristic indicators for rapid and unambiguous localization of the Pt-binding sites to certain amino acid residues. The method was then successfully applied to interpret the top-down ECD spectrum of an inter-chain Pt-crosslinked insulin dimer, insulin + Pt(NH3)2 + insulin (>10 kDa). In addition, ion mobility MS shows that Pt binds to multiple sites in Substance P, generating multiple conformers, which can be partially localized by collisionally activated dissociation (CAD). Platinum(II) (Pt(II)) was found to coordinate to amine groups of Arg and Lys, but not to disulfide bonds under the conditions used. The coordination of Pt to Arg or Lys appears to arise from the migration of Pt(II) from Met(S) as shown by monitoring the reaction products at different pH values by ECD. No direct binding of cisplatin to amine groups was observed at pH 3 ~ 10 unless Met residues were present in the sequence, but noncovalent interactions between cisplatin hydrolysis and amination [Pt(NH3)4](2+) products and these peptides were found regardless of pH.
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Affiliation(s)
- Huilin Li
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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22
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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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23
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Schennach M, Breuker K. Proteins with Highly Similar Native Folds Can Show Vastly Dissimilar Folding Behavior When Desolvated. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306838] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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24
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Schennach M, Breuker K. Proteins with highly similar native folds can show vastly dissimilar folding behavior when desolvated. Angew Chem Int Ed Engl 2013; 53:164-8. [PMID: 24259450 PMCID: PMC4065370 DOI: 10.1002/anie.201306838] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/07/2013] [Indexed: 01/08/2023]
Abstract
Proteins can be exposed to vastly different environments such as the cytosol or membranes, but the delicate balance between external factors and intrinsic determinants of protein structure, stability, and folding is only poorly understood. Here we used electron capture dissociation to study horse and tuna heart Cytochromes c in the complete absence of solvent. The significantly different stability of their highly similar native folds after transfer into the gas phase, and their strikingly different folding behavior in the gas phase, can be rationalized on the basis of electrostatic interactions such as salt bridges. In the absence of hydrophobic bonding, protein folding is far slower and more complex than in solution.
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Affiliation(s)
- Moritz Schennach
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria) http://www.bioms-breuker.at
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25
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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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26
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Shaw JB, Kaplan DA, Brodbelt JS. Activated ion negative electron transfer dissociation of multiply charged peptide anions. Anal Chem 2013; 85:4721-8. [PMID: 23577957 DOI: 10.1021/ac4005315] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the implementation and evaluation of activated ion negative electron transfer dissociation (AI-NETD) in order to enhance the analytical capabilities of NETD for the elucidation of doubly deprotonated peptide anions. The analytical figures-of-merit and fragmentation characteristics are compared for NETD alone and with supplemental collisional activation of the charge reduced precursors or infrared photoactivation of the entire ion population during the NETD reaction period. The addition of supplemental collisional activation of charge reduced precursor ions or infrared photoactivation of the entire ion population concomitant with the NETD reaction period significantly improves sequencing capabilities for peptide anions as evidenced by the greater abundances of product ions and overall sequence coverage. Neither of these two AI-NETD methods significantly alters the net fragmentation efficiencies relative to NETD; however, the sequence ion conversion percentages with respect to formation of diagnostic product ions are notably higher. Supplemental infrared photoactivation outperforms collisional activation for most of the peptide fragmentation metrics evaluated.
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Affiliation(s)
- Jared B Shaw
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, United States
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27
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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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28
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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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29
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Robb DB, Rogalski JC, Kast J, Blades MW. Liquid chromatography-atmospheric pressure electron capture dissociation mass spectrometry for the structural analysis of peptides and proteins. Anal Chem 2012; 84:4221-6. [PMID: 22494041 DOI: 10.1021/ac300648g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atmospheric pressure electron capture dissociation (AP-ECD) is an emerging technique with the potential to be a more accessible alternative to conventional ECD/electron transfer dissociation (ETD) methods because it can be implemented using a stand-alone ion source device suitable for use with any existing or future electrospray ionization mass spectrometer. With AP-ECD, no modification of the main instrument is required, so it may easily be retrofitted to instruments not originally equipped with ECD/ETD capabilities. Here, we present our first purpose-built AP-ECD source and demonstrate its use in conjunction with capillary LC for the analysis of substance P, a tryptic digest of bovine serum albumin, and a phosphopeptide mixture. Quality ECD spectra were obtained for all the samples at the low femtomole level, proving that LC-AP-ECD-MS is suitable for the structural analysis of peptides and protein digests, in this case using an unmodified quadrupole time-of-flight mass spectrometer built ca. 2002.
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Affiliation(s)
- Damon B Robb
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1.
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30
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Madsen JA, Cheng RR, Kaoud TS, Dalby KN, Makarov DE, Brodbelt JS. Charge-site-dependent dissociation of hydrogen-rich radical peptide cations upon vacuum UV photoexcitation. Chemistry 2012; 18:5374-83. [PMID: 22431222 DOI: 10.1002/chem.201103534] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Indexed: 11/06/2022]
Abstract
Here, 193 nm vacuum ultraviolet photodissociation (VUVPD) was used to investigate the fragmentation of hydrogen-rich radical peptide cations generated by electron transfer reactions. VUVPD offers new insight into the factors that drive radical- and photon-directed processes. The location of a basic Arg site influences photon-activated C(α)-C(O) bond cleavages of singly charged peptide radical cations, an outcome attributed to the initial conformation of the peptide as supported by molecular dynamics simulated annealing and the population of excited states upon UV excitation. This hybrid ETD/VUVPD method was employed to identify phosphorylation sites of the kinase domain of human TRPM7/ChaK1.
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Affiliation(s)
- James A Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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31
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Chen X, Fung YME, Chan WYK, Wong PS, Yeung HS, Chan TWD. Transition metal ions: charge carriers that mediate the electron capture dissociation pathways of peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2232-2245. [PMID: 21952786 DOI: 10.1007/s13361-011-0246-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/31/2011] [Accepted: 09/04/2011] [Indexed: 05/31/2023]
Abstract
Electron capture dissociation (ECD) of model peptides adducted with first row divalent transition metal ions, including Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+), were investigated. Model peptides with general sequence of ZGGGXGGGZ were used as probes to unveil the ECD mechanism of metalated peptides, where X is either V or W; and Z is either R or N. Peptides metalated with different divalent transition metal ions were found to generate different ECD tandem mass spectra. ECD spectra of peptides metalated by Mn(2+) and Zn(2+) were similar to those generated by ECD of peptides adducted with alkaline earth metal ions. Series of c-/z-type fragment ions with and without metal ions were observed. ECD of Fe(2+), Co(2+), and Ni(2+) adducted peptides yielded abundant metalated a-/y-type fragment ions; whereas ECD of Cu(2+) adducted peptides generated predominantly metalated b-/y-type fragment ions. From the present experimental results, it was postulated that electronic configuration of metal ions is an important factor in determining the ECD behavior of the metalated peptides. Due presumably to the stability of the electronic configuration, metal ions with fully-filled (i.e., Zn(2+)) and half filled (i.e., Mn(2+)) d-orbitals might not capture the incoming electron. Dissociation of the metal ions adducted peptides would proceed through the usual ECD channel(s) via "hot-hydrogen" or "superbase" intermediates, to form series of c-/z(•)- fragments. For other transition metal ions studied, reduction of the metal ions might occur preferentially. The energy liberated by the metal ion reduction would provide enough internal energy to generate the "slow-heating" type of fragment ions, i.e., metalated a-/y- fragments and metalated b-/y- fragments.
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Affiliation(s)
- Xiangfeng Chen
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
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32
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Robb DB, Rogalski JC, Kast J, Blades MW. A new ion source and procedures for atmospheric pressure-electron capture dissociation of peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1699-1706. [PMID: 21952883 DOI: 10.1007/s13361-011-0202-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 06/23/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
We introduce a new atmospheric pressure-electron capture dissociation (AP-ECD) source in which conventional nanospray emitters are coupled with the source block and photoionization lamp of a PhotoSpray APPI source. We also introduce procedures for data collection and processing, aimed at maximizing the signal-to-background ratio of ECD products. Representative data from Substance P are presented to demonstrate the performance of the technique. Further, we demonstrate the effects of two important experimental variables, source temperature and vacuum-interface declustering potential (DP), on the method. Last, we show that even when a high source temperature is used to maximize efficiency, AP-ECD fragments of a model phosphorylated peptide retain the modification.
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Affiliation(s)
- Damon B Robb
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
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33
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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
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Zirah S, Afonso C, Linne U, Knappe TA, Marahiel MA, Rebuffat S, Tabet JC. Topoisomer differentiation of molecular knots by FTICR MS: lessons from class II lasso peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:467-479. [PMID: 21472565 DOI: 10.1007/s13361-010-0028-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/28/2010] [Accepted: 10/31/2010] [Indexed: 05/30/2023]
Abstract
Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminal macrolactam ring. The structural characterization of lasso structures and differentiation from their unthreaded topoisomers is not trivial and generally requires the use of complementary biochemical and spectroscopic methods. Here we investigated two antimicrobial peptides belonging to the class II lasso peptide family and their corresponding unthreaded topoisomers: microcin J25 (MccJ25), which is known to yield two-peptide product ions specific of the lasso structure under collision-induced dissociation (CID), and capistruin, for which CID does not permit to unambiguously assign the lasso structure. The two pairs of topoisomers were analyzed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) upon CID, infrared multiple photon dissociation (IRMPD), and electron capture dissociation (ECD). CID and ECD spectra clearly permitted to differentiate MccJ25 from its non-lasso topoisomer MccJ25-Icm, while for capistruin, only ECD was informative and showed different extent of hydrogen migration (formation of c•/z from c/z•) for the threaded and unthreaded topoisomers. The ECD spectra of the triply-charged MccJ25 and MccJ25-lcm showed a series of radical b-type product ions (b'/•(n)). We proposed that these ions are specific of cyclic-branched peptides and result from a dual c/z• and y/b dissociation, in the ring and in the tail, respectively. This work shows the potentiality of ECD for structural characterization of peptide topoisomers, as well as the effect of conformation on hydrogen migration subsequent to electron capture.
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Affiliation(s)
- Séverine Zirah
- National Museum of Natural History, Communication Molecules and Adaptation of Micro-organisms, FRE 3206 CNRS - MNHN, CP 54, 57 rue Cuvier, F-75005 Paris, France.
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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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Yin S, Loo JA. Elucidating the site of protein-ATP binding by top-down mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:899-907. [PMID: 20163968 DOI: 10.1016/j.jasms.2010.01.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 01/08/2010] [Accepted: 01/08/2010] [Indexed: 05/11/2023]
Abstract
A Fourier-transform ion cyclotron resonance (FT-ICR) top-down mass spectrometry strategy for determining the adenosine triphosphate (ATP)-binding site on chicken adenylate kinase is described. Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS), but the ability to detect protein-ligand complexes depends on their stability in the gas phase. Previously, we showed that collisionally activated dissociation (CAD) of protein-nucleotide triphosphate complexes yield products from the dissociation of a covalent phosphate bond of the nucleotide with subsequent release of the nucleotide monophosphate (Yin, S. et al., J. Am. Soc. Mass Spectrom. 2008, 19, 1199-1208). The intrinsic stability of electrostatic interactions in the gas phase allows the diphosphate group to remain noncovalently bound to the protein. This feature is exploited to yield positional information on the site of ATP-binding on adenylate kinase. CAD and electron capture dissociation (ECD) of the adenylate kinase-ATP complex generate product ions bearing mono- and diphosphate groups from regions previously suggested as the ATP-binding pocket by NMR and crystallographic techniques. Top-down MS may be a viable tool to determine the ATP-binding sites on protein kinases and identify previously unknown protein kinases in a functional proteomics study.
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Affiliation(s)
- Sheng Yin
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, USA
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Li X, Lin C, O'Connor PB. Glutamine deamidation: differentiation of glutamic acid and gamma-glutamic acid in peptides by electron capture dissociation. Anal Chem 2010; 82:3606-15. [PMID: 20373761 PMCID: PMC2872026 DOI: 10.1021/ac9028467] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Due to its much slower deamidation rate compared to that of asparagine (Asn), studies on glutamine (Gln) deamidation have been scarce, especially on the differentiation of its isomeric deamidation products: alpha- and gamma-glutamic acid (Glu). It has been shown previously that electron capture dissociation (ECD) can be used to generate diagnostic ions for the deamidation products of Asn: aspartic acid (Asp) and isoaspartic acid (isoAsp). The current study explores the possibility of an extension of this ECD based method to the differentiation of the alpha- and gamma-Glu residues, using three human Crystallin peptides (alphaA (1-11), betaB2 (4-14), and gammaS (52-71)) and their potentially deamidated forms as model peptides. It was found that the z(*)-72 ions can be used to both identify the existence and locate the position of the gamma-Glu residues. When the peptide contains a charge carrier near its N-terminus, the c+57 and c+59 ions may also be generated at the gamma-Glu residue. It was unclear whether formation of these N-terminal diagnostic ions is specific to the Pro-gamma-Glu sequence. Unlike the Asp containing peptides, the Glu containing peptides generally do not produce diagnostic side chain loss ions, due to the instability of the resulting radical. The presence of Glu residue(s) may be inferred from the observation of a series of z(n)(*)-59 ions, although it was neither site specific nor without interference from the gamma-Glu residues. Finally, several interference peaks exist in the ECD spectra, which highlights the importance of the use of high performance mass spectrometers for confident identification of gamma-Glu residues.
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Affiliation(s)
- Xiaojuan Li
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Peter B. O'Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
- Department of Chemistry, University of Warwick, Coventry, UK
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Li X, Lin C, Han L, Costello CE, O’Connor PB. Charge remote fragmentation in electron capture and electron transfer dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:646-56. [PMID: 20171118 PMCID: PMC2882803 DOI: 10.1016/j.jasms.2010.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 01/03/2010] [Accepted: 01/12/2010] [Indexed: 05/04/2023]
Abstract
Secondary fragmentations of three synthetic peptides (human alphaA crystallin peptide 1-11, the deamidated form of human betaB2 crystallin peptide 4-14, and amyloid beta peptide 25-35) were studied in both electron capture dissociation (ECD) and electron-transfer dissociation (ETD) mode. In ECD, in addition to c and z. ion formations, charge remote fragmentations (CRF) of z. ions were abundant, resulting in internal fragment formation or partial/entire side-chain losses from amino acids, sometimes several residues away from the backbone cleavage site, and to some extent multiple side-chain losses. The internal fragments were observed in peptides with basic residues located in the middle of the sequences, which was different from most tryptic peptides with basic residues located at the C-terminus. These secondary cleavages were initiated by hydrogen abstraction at the alpha-, beta-, or gamma-position of the amino acid side chain. In comparison, ETD generates fewer CRF fragments than ECD. This secondary cleavage study will facilitate ECD/ETD spectra interpretation, and help de novo sequencing and database searching.
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Affiliation(s)
- Xiaojuan Li
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Liang Han
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Catherine E. Costello
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
- Department of Chemistry, University of Warwick, Coventry, UK
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Ledvina AR, McAlister GC, Gardner MW, Smith SI, Madsen JA, Schwartz JC, Stafford GC, Syka JEP, Brodbelt JS, Coon JJ. Infrared photoactivation reduces peptide folding and hydrogen-atom migration following ETD tandem mass spectrometry. Angew Chem Int Ed Engl 2010; 48:8526-8. [PMID: 19795429 DOI: 10.1002/anie.200903557] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron R Ledvina
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1322, USA
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Jensen CS, Wyer JA, Nielsen SB. Electron capture induced dissociation of dipeptide dications: where does the charge go? Phys Chem Chem Phys 2010; 12:12961-3. [DOI: 10.1039/c0cp00592d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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Ledvina A, McAlister G, Gardner M, Smith S, Madsen J, Schwartz J, Stafford G, Syka J, Brodbelt J, Coon J. Infrared Photoactivation Reduces Peptide Folding and Hydrogen-Atom Migration following ETD Tandem Mass Spectrometry. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903557] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Jensen CS, Holm AIS, Zettergren H, Overgaard JB, Hvelplund P, Nielsen SB. On the charge partitioning between c and z fragments formed after electron-capture induced dissociation of charge-tagged Lys-Lys and Ala-Lys dipeptide dications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1881-1889. [PMID: 19651526 DOI: 10.1016/j.jasms.2009.06.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 06/21/2009] [Accepted: 06/22/2009] [Indexed: 05/28/2023]
Abstract
Here we report on the charge partition between c and z fragments formed after femtosecond collisional electron-transfer from Cs atoms to charge-tagged peptide dications. Peptides chosen for study were Ala-Lys (AK) and Lys-Lys (KK) where one or both of the lysine epsilon-amino groups were trimethylated to provide one or two fixed charges. For peptides with only one charge tag, the other charge was obtained by protonation of an amino group. In some experiments the ammonium group was tagged by 18-crown-6-ether (CE). Since recombination energies decrease in the order: MeNH3+ > NMe4+ > MeNH3+(CE) > NMe4+(CE), it is possible to change the probability for the transferred electron to end up at either the N-terminal or the C-terminal residue by CE attachment. We find, however, that the individual recombination energies have little influence on the relative ratio between the yield of c and z ions as long as there are no mobile protons that can be transferred between the two fragments. Our results can be accounted for by the Utah-Washington model where the electron is captured into an amide pi* orbital that weakens the N-C(alpha) bond and causes its breakage, followed by proton, electron, or hydrogen transfer between the c and z fragments that stay together as an ion-molecule complex for some time. The data are also in accordance with the notion that an amide group competes with the charged groups for the electron. Electron capture by charged groups results in loss of small neutrals such as hydrogen and ammonia.
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Bushey JM, Baba T, Glish GL. Simultaneous collision induced dissociation of the charge reduced parent ion during electron capture dissociation. Anal Chem 2009; 81:6156-64. [PMID: 19572558 PMCID: PMC3141179 DOI: 10.1021/ac900627n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A method of performing collision induced dissociation (CID) on the charge-reduced parent ion as it is formed during electron capture dissociation (ECD), called ECD+CID, is described. In ECD+CID, the charge-reduced parent ion is selectively activated using resonant excitation and collisions with the helium bath gas inside a linear quadrupole ion trap ECD device (ECD(LIT)). It has been observed that ECD+CID can improve the sequence coverage for beta-endorphin over performing ECD alone (i.e., from 72 to 97%). Perhaps just as important, ECD+CID can be used to reduce the extent of multiple electron capture events observed when performing ECD in the ECD(LIT). Consequently, the abundance of mass-to-charge ratios corresponding to ECD product ions that contain neutralized protons is decreased, simplifying the interpretation of the product ion spectrum.
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Affiliation(s)
- Jared M. Bushey
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | - Takashi Baba
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
- Biosystem Research Development, Life Science Research Laboratory in Central Research Laboratory, Hitachi Ltd., 1-280, Higashi-Koigakubo, Kokubunji 185-8601, Japan
| | - Gary L. Glish
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
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Mikhailov VA, Cooper HJ. Activated Ion Electron Capture Dissociation (AI ECD) of proteins: synchronization of infrared and electron irradiation with ion magnetron motion. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:763-71. [PMID: 19200749 PMCID: PMC2674148 DOI: 10.1016/j.jasms.2008.12.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 12/15/2008] [Accepted: 12/17/2008] [Indexed: 05/12/2023]
Abstract
Here, we show that to perform activated ion electron capture dissociation (AI-ECD) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a CO(2) laser, it is necessary to synchronize both infrared irradiation and electron capture dissociation with ion magnetron motion. This requirement is essential for instruments in which the infrared laser is angled off-axis, such as the Thermo Finnigan LTQ FT. Generally, the electron irradiation time required for proteins is much shorter (ms) than that required for peptides (tens of ms), and the modulation of ECD, AI ECD, and infrared multiphoton dissociation (IRMPD) with ion magnetron motion is more pronounced. We have optimized AI ECD for ubiquitin, cytochrome c, and myoglobin; however the results can be extended to other proteins. We demonstrate that pre-ECD and post-ECD activation are physically different and display different kinetics. We also demonstrate how, by use of appropriate AI ECD time sequences and normalization, the kinetics of protein gas-phase refolding can be deconvoluted from the diffusion of the ion cloud and measured on the time scale longer than the period of ion magnetron motion.
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Affiliation(s)
| | - Helen J. Cooper
- Address reprint requests to Dr. Helen J. Cooper, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Ben Hamidane H, Chiappe D, Hartmer R, Vorobyev A, Moniatte M, Tsybin YO. Electron capture and transfer dissociation: Peptide structure analysis at different ion internal energy levels. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:567-575. [PMID: 19112028 DOI: 10.1016/j.jasms.2008.11.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 10/24/2008] [Accepted: 11/20/2008] [Indexed: 05/27/2023]
Abstract
We decoupled electron-transfer dissociation (ETD) and collision-induced dissociation of charge-reduced species (CRCID) events to probe the lifetimes of intermediate radical species in ETD-based ion trap tandem mass spectrometry of peptides. Short-lived intermediates formed upon electron transfer require less energy for product ion formation and appear in regular ETD mass spectra, whereas long-lived intermediates require additional vibrational energy and yield product ions as a function of CRCID amplitude. The observed dependencies complement the results obtained by double-resonance electron-capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and ECD in a cryogenic ICR trap. Compared with ECD FT-ICR MS, ion trap MS offers lower precursor ion internal energy conditions, leading to more abundant charge-reduced radical intermediates and larger variation of product ion abundance as a function of vibrational post-activation amplitude. In many cases decoupled CRCID after ETD exhibits abundant radical c-type and even-electron z-type ions, in striking contrast to predominantly even-electron c-type and radical z-type ions in ECD FT-ICR MS and especially activated ion-ECD, thus providing a new insight into the fundamentals of ECD/ETD.
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Affiliation(s)
- Hisham Ben Hamidane
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Li X, Cournoyer JJ, Lin C, O’Connor PB. The effect of fixed charge modifications on electron capture dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1514-26. [PMID: 18657441 PMCID: PMC3116146 DOI: 10.1016/j.jasms.2008.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 05/20/2008] [Accepted: 06/20/2008] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation (ECD) studies of two modified amyloid beta peptides (20-29 and 25-35) were performed to investigate the role of H* radicals in the ECD of peptide ions and the free-radical cascade (FRC) mechanism. 2,4,6-Trimethylpyridinium (TMP) was used as the fixed charge tag, which is postulated to both trap the originally formed radical upon electron capture and inhibit the H* generation. It was found that both the number and locations of the fixed charge groups influenced the backbone and side-chain cleavages of these peptides in ECD. In general, the frequency and extent of backbone cleavages decreased and those of side-chain cleavages increased with the addition of fixed charge tags. A singly labeled peptide with the tag group farther away from the protonated site experienced a smaller abundance decrease in backbone cleavage fragments than the one with the tag group closer to the protonated site. Despite the nonprotonated nature of all charge carriers in doubly labeled peptide ions, several c and z* ions were still observed in their ECD spectra. Thus, although H* transfer may be important for the NC(alpha) bond cleavage, there also exist other pathways, which would require a radical migration via H* abstraction through space or via an amide superbase mechanism. Finally, internal fragment ions were observed in the ECD of these linear peptides, indicating that the important role of the FRC in backbone cleavages is not limited to the ECD of cyclic peptides.
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Affiliation(s)
- Xiaojuan Li
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Jason J. Cournoyer
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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Creese AJ, Cooper HJ. The effect of phosphorylation on the electron capture dissociation of peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1263-74. [PMID: 18585055 PMCID: PMC2570175 DOI: 10.1016/j.jasms.2008.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 05/15/2008] [Accepted: 05/16/2008] [Indexed: 05/13/2023]
Abstract
The effect of site and frequency of phosphorylation on the electron capture dissociation of peptide ions has been investigated. The ECD of a suite of synthetic peptides (APLSFRGSLPKSYVK; one unmodified, three singly-phosphorylated, three-doubly phosphorylated, and one triply-phosphorylated); two tryptic phosphopeptides (YKVPQLEIVPN(p)SAEER, alpha-casein and FQ(p)SEEQQQTEDELQDK, beta-casein) and their unmodified counterparts, were determined over a range of ECD cathode potentials. The results show that, for doubly-charged precursor ions, the presence of phosphorylation has a deleterious effect on ECD sequence coverage. The fragmentation patterns observed suggest that for peptides with multiple basic residues, the phospho-groups exist in their deprotonated form and form salt-bridges with protonated amino acid side chains. The fragmentation observed for the acidic tryptic peptides suggested the presence of noncovalent interactions, which were perturbed on phosphorylation. Increasing the ECD electron energy significantly improves sequence coverage. Alternatively, improved sequence coverage can be achieved by performing ECD on triply-charged precursor ions. The findings are important for the understanding of gas-phase fragmentation of phosphopeptides.
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Affiliation(s)
| | - Helen J. Cooper
- Address reprint requests to Dr. H. J. Cooper, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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Tsybin YO, Quinn JP, Tsybin OY, Hendrickson CL, Marshall AG. Electron capture dissociation implementation progress in Fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:762-771. [PMID: 18359246 DOI: 10.1016/j.jasms.2008.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 02/13/2008] [Accepted: 02/14/2008] [Indexed: 05/26/2023]
Abstract
Successful electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) applications to peptide and protein structural analysis have been enabled by constant progress in implementation of improved electron injection techniques. The rate of ECD product ion formation has been increased to match the liquid chromatography and capillary electrophoresis timescales, and ECD has been combined with infrared multiphoton dissociation in a single experimental configuration to provide simultaneous irradiation, fast switching between the two techniques, and good spatial overlap between ion, photon, and electron beams. Here we begin by describing advantages and disadvantages of the various existing electron injection techniques for ECD in FT-ICR MS. We next compare multiple-pass and single-pass ECD to provide better understanding of ECD efficiency at low and high negative cathode potentials. We introduce compressed hollow electron beam injection to optimize the overlap of ion, photon, and electron beams in the ICR ion trap. Finally, to overcome significant outgassing during operation of a powerful thermal cathode, we introduce nonthermal electron emitter-based electron injection. We describe the first results obtained with cold cathode ECD, and demonstrate a general way to obtain low-energy electrons in FT-ICR MS by use of multiple-pass ECD.
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Affiliation(s)
- Yury O Tsybin
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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