Peptide backbone fragmentation initiated by side-chain loss at cysteine residue in matrixassisted laser desorption/ionization in-source decay mass spectrometry
[en] Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is initiated by hydrogen transfer from matrix molecules to the carbonyl oxygen of peptide backbone with subsequent radical-induced cleavage leading to c0/z• fragments pair. MALDI-ISD is a very powerful method to obtain long sequence tags from proteins or to do de novo sequencing of peptides. Besides classical fragmentation, MALDI-ISD also shows specific fragments for which the mechanism of formation enlightened the MALDI-ISD process. In this study, the MALDI-ISD mechanism is reviewed, and a specific mechanism is studied in details: the N-terminal side of Cys residue (Xxx-Cys) is described to promote the generation of c0 and w fragments in MALDI-ISD. Our data suggest that for sequences containing Xxx-Cys motifs, the N–Ca bond cleavage occurs following the hydrogen attachment to the thiol group of Cys side-chain. The c•/w fragments pair is formed by side-chain loss of the Cys residue with subsequent radical-induced cleavage
at the N–Ca bond located at the left side (N-terminal direction) of the Cys residue. This fragmentation pathway preferentially
occurs at free Cys residue and is suppressedwhen the cysteines are involved in disulfide bonds. Hydrogen attachment to alkylated Cys residues using iodoacetamide gives free Cys residue by the loss of •CH2CONH2 radical. The presence of alkylated Cys residue also suppress the formation of c•/w fragments pair via the (Cb)-centered radical, whereas w fragment is still observed as intense signal. In this case, the z• fragment formed by hydrogen attachment of carbonyl oxygen followed side-chain loss at alkylated Cys leads to a w fragment. Hydrogen attachment on peptide backbone and side-chain of Cys residue occurs therefore competitively
during MALDI-ISD process.
Disciplines :
Chemistry
Author, co-author :
Asakawa, Daiki
Smargiasso, Nicolas ; Université de Liège - ULiège > Département de chimie (sciences) > GIGA-R : Laboratoire de spectrométrie de masse (L.S.M.)
Quinton, Loïc ; Université de Liège - ULiège > Département de chimie (sciences) > Chimie biologique
De Pauw, Edwin ; Université de Liège - ULiège > Département de chimie (sciences) > GIGA-R : Laboratoire de spectrométrie de masse (L.S.M.)
Language :
English
Title :
Peptide backbone fragmentation initiated by side-chain loss at cysteine residue in matrixassisted laser desorption/ionization in-source decay mass spectrometry
Publication date :
2013
Journal title :
Journal of Mass Spectrometry
ISSN :
1076-5174
eISSN :
1096-9888
Publisher :
John Wiley & Sons, Inc, Chichester, United Kingdom
M. Karas, F. Hillenkamp,. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 1988, 60, 2299-2301.
W. J. Henzel, T. M. Billeci, J. T. Stults, S. C. Wong, C. Grimley, C. Watanabe,. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5011-5015.
D. J. C. Pappin, P. Hojrup, A. J. Bleasby,. Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 1993, 3, 327-332.
B. Paizs, S. Suhai,. Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 2005, 24, 508-548.
R. S. Brown, J. J. Lennon,. Sequence-specific fragmentation of matrix-assisted laser-desorbed protein/peptide ions. Anal. Chem. 1995, 67, 3990-3999.
D. C. Reiber, T. A. Grover, R. S. Brown,. Identifying proteins using matrix-assisted laser desorption/ionization in-source fragmentation data combined with database searching. Anal. Chem. 1998, 70, 673-683.
V. Katta, D. T. Chow, M. F. Rohde,. Applications of in-source fragmentation of protein ions for direct sequence analysis by delayed extraction MALDI-TOF mass spectrometry. Anal. Chem. 1998, 70, 4410-4416.
D. Debois, N. Smargiasso, K. Demeure, D. Asakawa, T. Zimmerman, L. Quinton, E. De Pauw,. MALDI in-source decay, from sequencing to imaging. Top. Curr. Chem. in press, DOI: 10.1007/128- 201 2-363.
J. J. Lennon, K. A. Walsh, Locating and identifying posttranslational modifications by in-source decay during MALDI-TOF mass spectrometry. Protein Sci. 1999, 8, 2487-2493.
D. Debois, V. Bertrand, L. Quinton, M.-C. De Pauw-Gillet, E. De Pauw,. MALDI-in source decay applied to mass spectrometry imaging: a new tool for protein identification. Anal. Chem. 2010, 82, 4036-4045.
D. Calligaris, R. Longuespée, D. Debois, D. Asakawa, A. Turtoi, V. Castronovo, A. Noel, V. Bertrand, M.-C. De Pauw-Gillet, E. De Pauw,. Selected protein monitoring in histological sections by targeted MALDI-FTICR in-source decay imaging. Anal. Chem. 2013, 85, 2117-2126.
B. Spengler, D. Kirsch, R. Kaufmann, E. Jaeger,. Peptide sequencing by matrix-assisted laser-desorption mass spectrometry. Rapid Commun. Mass Spectrom. 1992, 6, 105-108.
P. Chaurand, F. Luetzenkirchen, B. Spengler,. Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom. 1999, 10, 91-103.
D. Suckau, A. Resemann,. T3-sequencing: targeted characterization of the N- and C-termini of undigested proteins by mass spectrometry. Anal. Chem. 2003, 75, 5817-5824.
L. Sellami, O. Belgacem, C. Villard, M. E. Openshaw, P. Barbier, D. Lafitte,. In-source decay and pseudo tandem mass spectrometry fragmentation processes of entire high mass proteins on a hybrid vacuum matrix-assisted laser desorption ionization-quadrupole ion-trap time-of-flight mass spectrometer. Anal. Chem. 2012, 84, 5180-5185.
R. A. Zubarev, N. A. Kruger, F. W. McLafferty,. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 1998, 120, 3265-3266.
J. E. Syka, J. J. Coon, M. J. Schroeder, J. Shabanovitz, D. F. Hunt,. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9528-9533.
R. A. Zubarev,. Reactions of polypeptide ions with electrons in the gas phase, Mass Spectrom. Rev. 2003, 22, 57-77.
M. Takayama,. N-Cα bond cleavage of the peptide backbone via hydrogen abstraction. J. Am. Soc. Mass Spectrom. 2001, 12, 1044-1049.
J. Hardouin,. Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry. Mass Spectrom. Rev. 2007, 26, 672-682.
K. Demeure, L. Quinton, V. Gabelica, E. De Pauw,. Rational selection of the optimum MALDI matrix for top-down proteomics by in-source decay. Anal. Chem. 2007, 79, 8678-8685.
L. Quinton, K. Demeure, R. Dobson, N. Gilles, V. Gabelica, E. De Pauw,. New method for characterizing highly disulfide-bridged peptides in complex mixtures: application to toxin identification from crude venoms. J. Proteome Res. 2007, 6, 3216-3223.
D. Asakawa, D. Calligaris, N. Smargiasso, E. De Pauw,. Ultraviolet laser induced hydrogen transfer reaction: study of the first step of MALDI in-source decay mass spectrometry. J. Phys. Chem. B, 2013, DOI: 10.1021/jp311464k.
T. Köcher, Å. Engström, R. A. Zubarev,. Fragmentation of peptides in MALDI in-source decay mediated by hydrogen radicals. Anal. Chem. 2005, 77, 172-177.
D. Asakawa, N. Smargiasso, E. De Pauw,. Discrimination of isobaric Leu/Ile residues by MALDI in-source decay mass spectrometry. J. Am. Soc. Mass Spectrom. 2013, 24, 297-300.
D. Asakawa, M. Sakakura, M. Takayama,. Influence of initial velocity of analytes on in-source decay products in MALDI mass spectrometry using salicylic acid derivative matrices. Int. J. Mass Spectrom. 2013, 337, 29-33.
B. Spengler, D. Kirsch,. On the formation of initial ion velocities in matrix-assisted laser desorption ionization: virtual desorption time as an additional parameter describing ion ejection dynamics, Int. J. Mass Spectrom. 2003, 226, 71-83.
H. Han, Y. Xia, S. A. McLuckey,. Ion trap collisional activation of c and ż ions formed via gas-phase ion/ion electron-transfer dissociation, J. Proteome Res. 2007, 6, 3062-3069.
K. Demeure, V. Gabelica, E. De Pauw,. New advances in the understanding of the in-source decay fragmentation of peptides in MALDI-TOF-MS. J. Am. Soc. Mass Spectrom. 2010, 21, 1906-1917.
M. Sakakura, M. Takayama,. In-source decay and fragmentation characteristics of peptides using 5-aminosalicylic acid as a matrix in matrix-assisted laser desorption/ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 2010, 21, 979-988.
I. Osaka, M. Sakai, M. Takayama,. 5-Amino-1-naphthol, a novel 1,5-naphthalene derivative matrix suitable for matrix-assisted laser desorption/ionization in-source decay of phosphorylated peptides. Rapid Commun. Mass Spectrom. 2013, 27, 103-108.
N. Smargiasso, L. Quinton, E. De Pauw,. 2-Aminobenzamide and 2-aminobenzoic acid as new MALDI matrices inducing radical mediated in-source decay of peptides and proteins. J. Am. Soc. Mass Spectrom. 2012, 23, 469-474.
D. Calligaris, C. Villard, L. Terras, D. Braguer, P. Verdier-Pinard, D. Lafitte,. MALDI in-source decay of high mass protein isoforms: application to α- and β-tubulin variants. Anal. Chem. 2010, 82, 6176-6184.
D. Asakawa, M. Takayama,. Cα-C bond cleavage of the peptide backbone in MALDI in-source decay using salicylic acid derivative matrices. J. Am. Soc. Mass Spectrom. 2011, 22, 1224-1233.
D. Asakawa, M. Takayama,. Fragmentation processes of hydrogen-deficient peptide radicals in matrix-assisted laser desorption/ionization in-source decay mass spectrometry. J. Phys. Chem. B 2012, 116, 4016-4023.
D. Asakawa, M. Takayama,. Specific cleavage at peptide backbone Cα-C and CO-N bonds during matrix-assisted laser desorption/ionization in-source decay mass spectrometry with 5-nitrosalicylic acid as the matrix. Rapid Commun. Mass Spectrom. 2011, 25, 2379-2383.
I. Anusiewicz, M. Jasionowski, P. Skurski, J. Simons,. Backbone and side-chain cleavages in electron detachment dissociation (EDD), J. Phys. Chem. A 2005, 109, 11332-11337.
D. Asakawa, M. Takayama,. Mass spectrometric characterization of phosphorylated peptides using MALDI in-source decay via redox reactions. J. Mass Spectrom. 2012, 47, 180-187.
B. A. Budnik, K. F. Haselmann, R. A. Zubarev,. Electron detachment dissociation of peptide di-anions: an electron-hole recombination phenomenon, Chem. Phys. Lett. 2001, 342, 299-302.
J. J. Coon, J. Shabanowitz, D. F. Hunt, J. E. P. Syka,. Electron transfer dissociation of peptide anions. J. Am. Soc. Mass Spectrom. 2005, 16, 880-882.
F. Kjeldsen, O. A. Silivra, I. A. Ivonin, K. F. Haselmann, M. Gorshkov, R. A. Zubarev,. Cα-C backbone fragmentation dominates in electron detachment dissociation of gas-phase polypeptide polyanions. Chemistry Eur. J. 2005, 11, 1803-1812.
Y. Fukuyama, S. Iwamoto, K. Tanaka,. Rapid sequencing and disulfide mapping of peptides containing disulfide bonds by using 1,5-diaminonaphthalene as a reductive matrix. J. Mass Spectrom. 2006, 41, 191-201.
L. Quinton, N. Gilles, E. De Pauw, TxXIIIA, an atypical homodimeric conotoxin found in the Conus textile venom. J. Proteomics 2009, 72, 219-226.
F.-G. Hanisch,. Top-down sequencing of O-glycoproteins by in-source decay matrix-assisted laser desorption ionization mass spectrometry for glycosylation site analysis. Anal. Chem. 2011, 83, 4829-4837.
R. A. Zubarev, N. A. Kruger, E. K. Fridriksson, M. A. Lewis, D. M. Horn, B. K. Carpenter, F. W. McLafferty,. Electron capture dissociation of gaseous multiply-charged proteins is favored at disulfide bonds and other sites of high hydrogen atom affinity. J. Am. Chem. Soc. 1999, 121, 2857-2862.
S. R. Cole, X. Ma, X. Zhang, Y. Xia, Electron transfer dissociation (ETD) of peptides containing intrachain disulfide bonds, J. Am. Soc. Mass Spectrom. 2012, 23, 310-320.
R. Kaneko, Y. Wada, Decomposition of protein nitrosothiolsin matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry. J. Mass Spectrom. 2003, 38, 526-530.