Novel C β-C γ bond cleavages of tryptophan-containing peptide radical cations

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 2, 2012, Pages 264-273

  Song, Tao ^a   Hao, Qiang ^a,b   Law, Chun Hin ^a   Siu, Chi Kit ^b   Chu, Ivan K ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

C C cleavages of tryptophan; Density functional theory calculations; Low energy collision induced dissociation; Peptide radical cations

Indexed keywords

BOND CLEAVAGES; CARBON ATOMS; CARBON RADICALS; DENSITY FUNCTIONAL THEORY CALCULATIONS; DISSOCIATION ENERGIES; HYDROGEN-ATOM TRANSFER; LEUCINE RESIDUES; LOW-ENERGY COLLISION-INDUCED DISSOCIATION; NEUTRAL RADICAL; NITROGEN ATOM; PRODUCT ION SPECTRA; RADICAL CATIONS; SIDE-CHAINS; THEORETICAL DENSITY; TRYPTOPHAN RESIDUES;

AMINO ACIDS; ATOMS; DENSITY FUNCTIONAL THEORY; DISSOCIATION; HYDROGEN; HYDROGEN BONDS; PEPTIDES; POSITIVE IONS;

FREE RADICAL REACTIONS;

1 METHYLTRYPTOPHAN; HYDROGEN; HYDROGEN DEFICIENT PEPTIDE RADICAL CATION; INDOLE; INDOLE NITROGEN; LEUCINE; NITROGEN; PEPTIDE; RADICAL; TRYPTOPHAN; TRYPTOPHAN DERIVATIVE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA CARBON GAMMA CARBON BOND; CHEMICAL BOND; COLLISIONALLY ACTIVATED DISSOCIATION; DEHYDROGENATION; DENSITY FUNCTIONAL THEORY; ENERGY; FRAGMENTATION REACTION; PROTEIN CLEAVAGE; PROTEIN STRUCTURE; PROTON TRANSPORT;

CATIONS; FREE RADICALS; MASS SPECTROMETRY; PEPTIDES; TRYPTOPHAN;

EID: 84856268393     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-011-0295-5     Document Type: Article

References (58)

1. R Aebersold DR Goodlett 2001 Mass spectrometry in proteomics Chem. Rev. 101 269 295 10.1021/cr990076h 1:CAS:528:DC%2BD3MXltlGlug%3D%3D (Pubitemid 32325797)
2. Stults, J.T.; Arnott, D.: In: Burlingame, A.L. (ed.) Academic Press, Methods Enzymol 402, 245-289 (2005)
3. O Burlet RS Orkiszewski KD Ballard SJ Gaskell MJ Bertrand 1992 Charge Promotion of Low-Energy Fragmentations of Peptide Ions Rapid Commun. Mass Spectrom. 6 658 662 10.1002/rcm.1290061106 1:CAS:528:DyaK3sXhtVantro%3D
4. JL Jones AR Dongré Á Somogyi VH Wysocki 1994 Sequence Dependence of Peptide Fragmentation Efficiency Curves Determined by Electrospray Ionization/Surface-Induced Dissociation Mass Spectrometry J. Am. Chem. Soc. 116 8368 8369 10.1021/ja00097a055 1:CAS:528:DyaK2MXlvVyqtA%3D%3D (Pubitemid 24981551)
5. AR Dongré JL Jones Á Somogyi VH Wysocki 1996 Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model J. Am. Chem. Soc. 118 8365 8374 10.1021/ja9542193 (Pubitemid 26305258)
6. G Tsaprailis H Nair Á Somogyi VH Wysocki W Zhong JH Futrell SG Summerfield SJ Gaskell 1999 Influence of Secondary Structure on the Fragmentation of Protonated Peptides J. Am. Chem. Soc. 121 5142 5154 10.1021/ja982980h 1:CAS:528:DyaK1MXjt1aru7o%3D (Pubitemid 29275721)
7. VH Wysocki G Tsaprailis LL Smith LA Breci 2000 Special Feature: Commentary - Mobile and Localized Protons: A Framework for Understanding Peptide Dissociation J. Mass Spectrom. 35 1399 1406 10.1002/1096-9888(200012)35: 12<1399::AID-JMS86>3.0.CO;2-R 1:CAS:528:DC%2BD3MXltFWrtQ%3D%3D (Pubitemid 32063646)
8. B Paizs S Suhai 2005 Fragmentation pathways of protonated peptides Mass Spectrom. Rev. 24 508 548 10.1002/mas.20024 1:CAS:528:DC%2BD2MXlvFShsLg%3D (Pubitemid 41083800)
9. Wysocki, V.H.; Cheng, G.; Zhang, Q.; Herrmann, K.A.; Beardsley, R.L.; Hilderbrand, A.E.: In: Laskin, J.; Lifshitz, C. (eds.) Principles of Mass Spectrometry Applied to Biomolecules, pp. 279-300. Wiley Interscience, New York (2006)
10. RS Johnson SA Martin K Biemann JT Stults JT Watson 1987 Novel Fragmentation Process of Peptides by Collision-Induced Decomposition in a Tandem Mass Spectrometer: Differentiation of Leucine and Isoleucine Anal. Chem. 59 2621 2625 10.1021/ac00148a019 1:CAS:528:DyaL2sXmtlOhtbw%3D
11. IA Papayannopoulos 1995 The Interpretation of Collision-Induced Dissociation Tandem Mass-Spectra of Peptides Mass Spectrom. Rev. 14 49 73 10.1002/mas.1280140104 1:CAS:528:DyaK28Xis1ShsQ%3D%3D
12. RA Zubarev DM Horn EK Fridriksson NL Kelleher NA Kruger MA Lewis BK Carpenter FW McLafferty 2000 Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations Anal. Chem. 72 563 573 10.1021/ac990811p 1:CAS:528:DC%2BD3cXmsFeg (Pubitemid 33595293)
13. RA Zubarev 2004 Electron-Capture Dissociation Tandem Mass Spectrometry Curr. Opin. Biotechnol. 15 12 16 10.1016/j.copbio.2003.12.002 1:CAS:528:DC%2BD2cXht12jt78%3D (Pubitemid 38224243)
14. H Cooper R Hudgins K Håkansson A Marshall 2002 Characterization of Amino Acid Side Chain Losses in Electron Capture Dissociation J. Am. Soc. Mass Spectrom. 13 241 249 10.1016/S1044-0305(01)00357-9 1:CAS:528: DC%2BD38XhsleqsL4%3D (Pubitemid 34552604)
15. YME Fung TWD Chan 2005 Experimental and Theoretical Investigations of the Loss of Amino Acid Side Chains in Electron Capture Dissociation of Model Peptides J. Am. Soc. Mass Spectrom. 16 1523 1535 10.1016/j.jasms.2005.05.001 1:CAS:528:DC%2BD2MXpt1WmsrY%3D (Pubitemid 41169861)
16. JEP Syka JJ Coon MJ Schroeder J Shabanowitz DF Hunt 2004 Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry Proc. Natl. Acad. Sci. U. S. A. 101 9528 9533 10.1073/pnas.0402700101 1:CAS:528:DC%2BD2cXlvVahs70%3D (Pubitemid 38869270)
17. JM Hogan SJ Pitteri PA Chrisman SA McLuckey 2005 Complementary Structural Information from a Tryptic N-Linked Glycopeptide via Electron Transfer Ion/Ion Reactions and Collision-Induced Dissociation J. Proteome Res. 4 628 632 10.1021/pr049770q 1:CAS:528:DC%2BD2MXitVClurc%3D (Pubitemid 40548173)
18. • Ions Formed via Gas-Phase Ion/Ion Electron-Transfer Dissociation J. Proteome Res. 6 3062 3069 10.1021/pr070177t 1:CAS:528: DC%2BD2sXntFKqtrs%3D (Pubitemid 47310191)
19. TW Chung F Tureček 2010 Backbone and Side-Chain Specific Dissociations of z Ions from Non-Tryptic Peptides J. Am. Soc. Mass Spectrom. 21 1279 1295 10.1016/j.jasms.2010.02.018 1:CAS:528:DC%2BC3cXps1eisLs%3D
20. QY Sun H Nelson T Ly BM Stoltz RR Julian 2009 Side Chain Chemistry Mediates Backbone Fragmentation in Hydrogen Deficient Peptide Radicals J. Proteome Res. 8 958 966 10.1021/pr800592t 1:CAS:528:DC%2BD1MXhtF0%3D
21. Hopkinson, A.C.; Siu, K.W.M.: Principles of Mass Spectrometry Applied to Biomolecules, pp. 301-335. Wiley Interscience, New York (2006)
22. AC Hopkinson 2009 Radical Cations of Amino Acids and Peptides: Structures and Stabilities Mass Spectrom. Rev. 28 655 671 10.1002/mas.20229 1:CAS:528:DC%2BD1MXos1WhsL8%3D
23. CK Barlow WD McFadyen RAJ O'Hair 2005 Formation of Cationic Peptide Radicals by Gas-Phase Redox Reactions with Trivalent Chromium, Manganese, Iron, and Cobalt Complexes J. Am. Chem. Soc. 127 6109 6115 10.1021/ja043088f 1:CAS:528:DC%2BD2MXis1Ogsbc%3D (Pubitemid 40584827)
24. J Laskin ZB Yang C Lam IK Chu 2007 Charge-Remote Fragmentation of Odd-Electron Peptide Ions Anal. Chem. 79 6607 6614 10.1021/ac070777b 1:CAS:528:DC%2BD2sXos1SktLs%3D (Pubitemid 47395045)
25. IK Chu CF Rodriquez TC Lau AC Hopkinson KWM Siu 2000 Molecular Radical Cations of Oligopeptides J. Phys. Chem. B 104 3393 3397 10.1021/jp994487d 1:CAS:528:DC%2BD3cXhslKitrg%3D
26. T Ly RR Julian 2008 Residue-Specific Radical-Directed Dissociation of Whole Proteins in the Gas Phase J. Am. Chem. Soc. 130 351 358 10.1021/ja076535a 1:CAS:528:DC%2BD2sXhsVaitLnN
27. Wee, S.; Mortimer, A.; Moran, D.; Wright, A.; Barlow, C.K.; O'Hair, R.A.J.; Radom, L.; Easton, C.J.: Gas-Phase Regiocontrolled Generation of Charged Amino Acid and Peptide Radicals. Chem. Commun. (Cambridge, UK) 4233-4235 (2006) (Pubitemid 44556368)
28. G Hao SS Gross 2006 Electrospray Tandem Mass Spectrometry Analysis of S- and N-Nitrosopeptides: Facile Loss of NO and Radical-Induced Fragmentation J. Am. Soc. Mass Spectrom. 17 1725 1730 10.1016/j.jasms.2006.07.026 1:CAS:528:DC%2BD28Xht1ykt7vP (Pubitemid 44809955)
29. V Ryzhov AKY Lam RAJ O'Hair 2009 Gas-Phase Fragmentation of Long-Lived Cysteine Radical Cations Formed Via NO Loss from Protonated S-Nitrosocysteine J. Am. Soc. Mass Spectrom. 20 985 995 10.1016/j.jasms.2008.12.026 1:CAS:528:DC%2BD1MXmtVegs7c%3D
30. ER Knudsen RR Julian 2010 Fragmentation Chemistry Observed in Hydrogen Deficient Radical Peptides Generated from N-nitrosotryptophan Residues Int. J. Mass Spectrom. 294 83 87 10.1016/j.ijms.2010.05.012 1:CAS:528: DC%2BC3cXos1Khsrw%3D
31. AKY Lam V Ryzhov RAJ O'Hair 2010 Mobile Protons Versus Mobile Radicals: Gas-Phase Unimolecular Chemistry of Radical Cations of Cysteine-Containing Peptides J. Am. Soc. Mass Spectrom. 21 1296 1312 10.1016/j.jasms.2010.01.027 1:CAS:528:DC%2BC3cXps1eisLg%3D
32. DS Masterson H Yin A Chacon DL Hachey JL Norris NA Porter 2003 Lysine Peroxycarbamates: Free Radical-Promoted Peptide Cleavage J. Am. Chem. Soc. 126 720 721 10.1021/ja038615u (Pubitemid 38114348)
33. R Hodyss HA Cox JL Beauchamp 2005 Bioconjugates for Tunable Peptide Fragmentation: Free Radical Initiated Peptide Sequencing (FRIPS) J. Am. Chem. Soc. 127 12436 12437 10.1021/ja052042z 1:CAS:528:DC%2BD2MXotFSitbc%3D (Pubitemid 41292131)
34. M Lee M Kang B Moon HB Oh 2009 Gas-phase peptide sequencing by TEMPO-mediated radical generation Analyst 134 1706 1712 10.1039/b904115j 1:CAS:528:DC%2BD1MXoslCksrw%3D
35. S Wee RAJ O'Hair WD McFadyen 2004 Comparing the Gas-Phase Fragmentation Reactions of Protonated and Radical Cations of the Tripeptides GXR Int. J. Mass Spectrom. 234 101 122 10.1016/j.ijms.2004.02.018 1:CAS:528:DC%2BD2cXktVWitLg%3D
36. E Bagheri-Majdi YY Ke G Orlova IK Chu AC Hopkinson KWM Siu 2004 Copper-Mediated Peptide Radical Ions in the Gas Phase J. Phys. Chem. B 108 11170 11181 10.1021/jp049531q 1:CAS:528:DC%2BD2cXltFOgsL4%3D
37. + Product Ions in Radical Peptide Ions Containing Tyrosine and Tryptophan: The Influence of Proton Affinities on Product Formation J. Am. Soc. Mass Spectrom. 19 1799 1807 10.1016/j.jasms.2008.09.026 1:CAS:528:DC%2BD1cXhsVyrtrjE
38. S Wee RAJ O'Hair WD McFadyen 2002 Side-Chain Radical Losses from Radical Cations Allows Distinction of Leucine and Isoleucine Residues in the Isomeric Peptides Gly-XXX-Arg Rapid Commun. Mass Spectrom. 16 884 890 10.1002/rcm.658 1:CAS:528:DC%2BD3sXht12ktrY%3D (Pubitemid 34456290)
39. J Laskin JH Futrell IK Chu 2007 Is Dissociation of Peptide Radical Cations an Ergodic Process? J. Am. Chem. Soc. 129 9598 9599 10.1021/ja073748r 1:CAS:528:DC%2BD2sXnslGqt7w%3D (Pubitemid 47237465)
40. D Moran R Jacob GPF Wood ML Coote MJ Davies RAJ O'Hair CJ Easton L Radom 2006 Rearrangements in Model Peptide-Type Radicals via Intramolecular Hydrogen-Atom Transfer Helv. Chim. Acta 89 2254 2272 10.1002/hlca.200690210 1:CAS:528:DC%2BD28Xht1Whu7%2FN (Pubitemid 44745759)
41. ZB Yang C Lam IK Chu J Laskin 2008 The Effect of the Secondary Structure on Dissociation of Peptide Radical Cations: Fragmentation of Angiotensin III and Its Analogues J. Phys. Chem. B 112 12468 12478 10.1021/jp805226x 1:CAS:528:DC%2BD1cXhtVymtL%2FO
42. DCM Ng T Song SO Siu CK Siu J Laskin IK Chu 2010 Formation, Isomerization, and Dissociation of α-Carbon-centered and π-Centered Glycylglycyltryptophan Radical Cations J. Phys. Chem. B 114 2270 2280 10.1021/jp908599a 1:CAS:528:DC%2BC3cXhtVSitbk%3D
43. T Song DCM Ng Q Quan C-K Siu IK Chu 2011 Arginine-Facilitated α- and π-Radical Migrations in Glycylarginyltryptophan Radical Cations Chem. Asian J. 6 888 898 10.1002/asia.201000677 1:CAS:528:DC%2BC3MXisVaitLY%3D
44. α-C Bond Cleavages of Aromatic-Containing Peptide Radical Cations Phys. Chem. Chem. Phys. 13 5888 5896 10.1039/c0cp00974a 1:CAS:528:DC%2BC3MXjt12isbo%3D
45. T Ly RR Julian 2009 Tracking Radical Migration in Large Hydrogen Deficient Peptides with Covalent Labels: Facile Movement does not Equal Indiscriminate Fragmentation J. Am. Soc. Mass Spectrom. 20 1148 1158 10.1016/j.jasms.2009.02.009 1:CAS:528:DC%2BD1MXmtVegsrw%3D
46. J Laskin Z Yang CMD Ng IK Chu 2010 Fragmentation of α-Radical Cations of Arginine-Containing Peptides J. Am. Soc. Mass Spectrom. 21 511 521 10.1016/j.jasms.2009.12.021 1:CAS:528:DC%2BC3cXjvFyntLo%3D
47. IK Chu J Zhao M Xu SO Siu AC Hopkinson KWM Siu 2008 Are the Radical Centers in Peptide Radical Cations Mobile? The Generation, Tautomerism, and Dissociation of Isomeric α-Carbon-centered Triglycine Radical Cations in the Gas Phase J. Am. Chem. Soc. 130 7862 7872 10.1021/ja801108j 1:CAS:528:DC%2BD1cXms1Gisr4%3D (Pubitemid 351875061)
48. S Wee RAJ O'Hair WD McFadyen 2006 The Role of the Position of the Basic Residue in the Generation and Fragmentation of Peptide Radical Cations Int. J. Mass Spectrom. 249 171 183 10.1016/j.ijms.2006.01.007
49. LY Zhang JP Reilly 2009 Radical-Driven Dissociation of Odd-Electron Peptide Radical Ions Produced in 157 nm Photodissociation J. Am. Soc. Mass Spectrom. 20 1378 1390 10.1016/j.jasms.2009.03.026 1:CAS:528: DC%2BD1MXotFOksLg%3D
50. MM Savitski ML Nielsen RA Zubarev 2007 Side-Chain Losses in Electron Capture Dissociation to Improve Peptide Identification Anal. Chem. 79 2296 2302 10.1021/ac0619332 1:CAS:528:DC%2BD2sXht1WqsbY%3D (Pubitemid 46449008)
51. Chan, W.C.; White, P.D.: Fmoc Solid Phase Peptide Synthesis: A Practical Approach, pp. 41-76. Oxford University Press, New York (2000)
52. 2O Inorg. Chem. 22 2858 2863 10.1021/ic00162a018 1:CAS:528:DyaL3sXltlalt7k%3D
53. SP Varkey C Ratnasamy P Ratnasamy 1998 Zeolite-Encapsulated Manganese(III)salen Complexes J. Mol. Catal. A Chem. 135 295 306 10.1016/S1381-1169(97)00307-5 1:CAS:528:DyaK1cXmsFGms7Y%3D (Pubitemid 28494650)
54. AD Becke 1993 Density-Functional Thermochemistry. III. The Role of Exact Exchange Chem. Phys. 98 5648 5652 1:CAS:528:DyaK3sXisVWgtrw%3D
55. WJ Hehre R Ditchfield JA Pople 1972 Self-Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules J. Chem. Phys. 56 2257 2261 10.1063/1.1677527 1:CAS:528:DyaE38XptVemsw%3D%3D
56. T Clark J Chandrasekhar GW Spitznagel PvR Schleyer 1983 Efficient Diffuse Function-Augmented Basis Sets for Anion Calculations. III. The 3-21+G Basis Set for First-Row Elements, Li-F J. Comput. Chem. 4 294 301 10.1002/jcc.540040303 1:CAS:528:DyaL3sXlt1ymsb8%3D
57. Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Montgomery, Jr.; J.A.; Vreven, T.; Kudin, K.N.; Burant, J.C.; Millam, J.M.; Iyengar, S.S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G.A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J.E.; Hratchian, H.P.; Cross, J.B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R.E.; Yazyev, O.; Austin, A.J.; Cammi, R.; Pomelli, C.; Ochterski, J.W.; Ayala, P.Y.; Morokuma, K.; Voth, G.A.; Salvador, P.; Dannenberg, J.J.; Zakrzewski, V.G.; Dapprich, S.; Daniels, A.D.; Strain, M.C.; Farkas, O.; Malick, D.K.; Rabuck, A.D.; Raghavachari, K.; Foresman, J.B.; Ortiz, J.V.; Cui, Q.; Baboul, A.G.; Clifford, S.; Cioslowski, J.; Stefanov, B.B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R.L.; Fox, D.J.; Keith, T.; Al-Laham, M.A.; Peng, C.Y.; Nanayakkara, A.; Challacombe, M.; Gill, P.M.W.; Johnson, B.; Chen, W.; Wong, M.W.; Gonzalez, C.; Pople, J.A.: Gaussian 03, Revision C.02; Gaussian, Inc.; Wallingford CT (2004)
58. H Zipse 2006 Radical stability - A theoretical perspective Top. Curr. Chem. 263 163 189 10.1007/128-028 1:CAS:528:DC%2BD28XmtFajsrg%3D (Pubitemid 44420777)