Peptide Fragmentation Overview

Principles of Mass Spectrometry Applied to Biomolecules

Volumn , Issue , 2006, Pages 277-300

  Wysocki, Vicki H ^a   Cheng, Guilong ^a   Zhang, Qingfen ^a   Herrmann, Kristin A ^a   Beardsley, Richard L ^a   Hilderbrand, Amy E ^a  

^a University of Arizona   (United States)

Author keywords

Accepted peptide fragmentation structures; Charge site influence on fragmentation; Peptide fragmentation knowledge in algorithm development

Indexed keywords

ALGORITHM DEVELOPMENT; CHARGE SITE INFLUENCE ON FRAGMENTATION; PEPTIDE FRAGMENTATION;

PEPTIDES;

EID: 84889841700     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/047005042X.ch8     Document Type: Chapter

References (80)

1. Ambihapathy K, Yalcin T, Leung H-W, Harrison AG (1997): Pathways to immonium ions in the fragmentation of protonated peptides. J. Mass Spectrom. 32:209-215.
2. Ballard KD, Gaskell SJ (1993): Dehydration of peptide [M+H]+ions in the gas phase. J. Am. Soc. Mass Spectrom. 4:477-481.
3. Beardsley RL, Reilly JP (2004): Fragmentation of amidinated peptide ions. J. Am. Soc. Mass Spectrom. 15:158-167.
4. Beardsley RL, Sharon LA, Reilly JP (2005): Peptide de novo sequencing facilitated by a duallabeling strategy. Anal. Chem. 77:6300-6309.
5. Biemann K (1988): Contributions of mass spectrometry to peptide and protein structure. Biomed. Environ. Mass Spectrom. 16:99-111.
6. Biemann K (1986): Mass spectrometric methods for protein sequencing. Anal. Chem. 58: 1288A-1300A.
7. Breci LA, Tabb DL, Yates JR, III, Wysocki VH (2003): Cleavage N-terminal to proline: Analysis of a database of peptide tandem mass spectra. Anal. Chem. 75:1963-1971.
8. Burlet O, Orkiszewski RS, Ballard KD, Gaskell SJ (1992): Charge promotion of low-energy fragmentations of peptide ions. Rapid Commun. Mass Spectrom. 6:658-662.
9. Chrisman PA, Pitteri SJ, McLuckey SA (2005): Parallel ion parking: Improving conversion of parents to first-generation products in electron transfer dissociation. Anal. Chem. 77: 3411-3414.
10. Cooks RG, Ast T, MabudMA (1990): Collisions of polyatomic ions with surfaces. Int. J. Mass Spectrom. Ion Proc. 100:209-265.
11. Csonka IP, Paizs B, Lendvay G, Suhai S (2000): Proton mobility in protonated peptides: A joint molecular orbital and RRKM study. Rapid Commun. Mass Spectrom. 14:417-431.
12. Dongre AR, Jones JL, Somogyi A, Wysocki VH (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.
13. Eckart K, Holthausen MC, Koch W, Spiess J (1998): Mass spectrometric and quantum mechanical analysis of gas-phase formation, structure, and decomposition of various b2 ions and their specifically deuterated analogs. J. Am. Soc. Mass Spectrom. 9:1002- 1011.
14. El Aribi H, Rodriquez CF, Almeida DRP, Ling Y, Mak WWN, Hopkinson AC, Siu MKW (2003): Elucidation of fragmentation mechanisms of Protonated peptide ions and their products: A case study on glycylglycylglycine using density functional theory and threshold collision-induced dissociation. J. Am. Chem. Soc. 125:9229-9236
15. El Aribi H, Orlova G, Rodriquez CF, Almeida DRP, Hopkinson AC, Siu MKW (2004): Fragmentation mechanisms of product ions from protonated tripeptides. J. Phys. Chem. B 108:18743-18749
16. Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP (2004): Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 22:214- 219.
17. Farrugia JM, O'Hair RAJ, Reid GE (2001): Do all b2 ions have oxazolone structures? Multistage mass spectrometry and ab initio studies on protonated N-acyl amino acid methyl ester model systems. Int. J. Mass Spectrom. 210/211:71-87.
18. Freitas MA, Marshall AG (1999): Rate and extent of gas-phase hydrogen/deuterium exchange of bradykinins: Evidence for peptide zwitterions in the gas phase. Int. J. Mass Spectrom. 182/183:221-231.
19. Ge Y, Horn DM, McLafferty FW (2001): Blackbody infrared radiative dissociation of larger(42KD) multiply charged proteins. Int. J. Mass Spectrom. 210/211:203-214.
20. Gu C, Tsaprailis G, Breci L,Wysocki VH (2000): Selective gas-phase cleavage at the peptide bond C-terminal to aspartic acid in fixed-charge derivatives of Asp-containing peptides. Anal. Chem. 72:5804-5813.
21. Harrison AG, Yalcin T (1997): Proton mobility in protonated amino acids and peptides. Int. J. Mass Spectrom. 165/166:339-347.
22. Herrmann KA,Wysocki VH, Vorpagel ER (2005): Computational investigation and hydrogen/ deuterium exchange of the fixed charge derivative Tris(2,4,6-trimethoxyphenyl) phosphonium: Implications for the aspartic acid cleavage mechanism. J. Am. Soc. Mass Spectrom. 16:1067-1080.
23. Huang Y, Triscari JM, Pasa-Tolic L, Anderson GA, Lipton MS, Smith RD, Wysocki VH (2004): Dissociation behavior of doubly-charged tryptic peptides: Correlation of gas-phase cleavage abundance with Ramachandran plots. J. Am. Chem. Soc. 126: 3034-3035.
24. Huang Y, Triscari JM, Tseng GC, Pasa-Tolic L, Lipton MS, Smith RD, Wysocki VH (2005): Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal. Chem. 77:7626-7638.
25. Huang Y, Wysocki VH, Tabb DL, Yates JR (2002): The influence of histidine on cleavage Cterminal to acidic residues in doubly protonated tryptic peptides. Int. J. Mass Spectrom. 219:233-244.
26. Hunt DF, Yates JR, Shabanowitz J, Winston S, Hauer CR (1986): Protein sequencing by tandem mass-spectrometry. Proc. Natl. Acad. Sci. USA 83:6233-6237.
27. Johnson RS, Krylov D,Walsh KA (1995): Proton mobility within electrosprayed peptide ions. J. Mass Spectrom. 30:386-387.
28. Johnson RS, Martin SA, Biemann K (1988): Collision-induced fragmentation of (M H) ions of peptides: Side chain specific sequence ions. Int. J. Mass Spectrom. Ion Proc. 86:137-154.
29. Jonsson AP, Bergman T, Jornvall H, Griffiths WJ (2001): Gln-Gly cleavage: A dominant dissociation site in the fragmentation of protonated peptides. Rapid Commun. Mass Spectrom. 15:713-720.
30. Kapp EA, Schuetz F, Reid GE, Eddes JS, Moritz RL, O'Hair RAJ, Speed TP, Simpson RJ (2003): Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 75:6251- 6264.
31. Kenny PTM, Nomoto K, Orlando R (1992): Fragmentation studies of peptides: The formation of y ions. Rapid Commun. Mass Spectrom. 6:95-97.
32. Keough T, Youngquist RS, Lacey MP (1999): A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry. Proc. Natl. Acad. Sci. USA 96:7131-7136.
33. Komaromi I, Somogyi A, Wysocki VH (2005): Proton migration and its effect on the MS fragmentation of N-acetyl OMe proline: MS/MS experiments and ab initio and density functional calculations. Int. J. Mass Spectrom. 241:315-323.
34. Kruger NA, Zubarev RA, Horn DM, McLafferty FW (1999): Electron capture dissociation of multiply charged peptide cations. Int. J. Mass Spectrom. 187:787-793.
35. Kulhanek P, Schlag EW, Koca J (2003): A novel mechanism of proton transfer in protonated peptides. J. Am. Chem. Soc. 125:13678-13679.
36. Lebrilla CB (2004): Profiling oligosaccharides diversity by infrared multiphoton dissociation. Abstracts of Papers, 227th ACS Nat. Meeting, Anaheim, CA, March 28-April 1, 2004, PHYS-050.
37. Liao P-C, Huang Z-H, Allison J (1997): Charge remote fragmentation of peptides following attachment of a fixed positive charge: A matrix-assisted laser desorption/ionization postsource decay study. J. Am. Soc. Mass Spectrom. 8:501-509.
38. Little DP, Speir JP, Senko MW, Oconnor PB, McLafferty FW (1994): Infrared multiphoton dissociation of large multiply-charged ions for biomolecule sequencing. Anal. Chem. 66:2809-2815.
39. Luo G, Marginean I, Vertes A (2002): Internal energy of ions generated by matrix-assisted laser desorption/ionization. Anal. Chem. 74:6185-6190.
40. Mabud MA, Dekrey MJ, Cooks RG (1985): Surface-induced dissociation of molecular ions. Int. J. Mass Spectrom. 67:285-294.
41. Martin SA, Hill JA, Kittrell C, Biemann K (1990): Photon-induced dissociation with a 4-sector tandem mass-spectrometer. J. Am. Soc. Mass Spectrom. 1:107-109.
42. McCormack AL, Somogyi A, Dongre AR, Wysocki VH (1993): Fragmentation of protonated peptides: Surface-induced dissociation in conjunction with a quantum mechanical approach. Anal. Chem. 65:2859-2872.
43. Mueller DR, Eckersley M, Richter WJ (1988): Hydrogen transfer-reactions in the formation of Y 2 sequence ions from protonated peptides. Org. Mass Spectrom. 23:217-222.
44. Nair H, Wysocki VH (1998): Are peptides without basic residues protonated primarily at the amino terminus? Int. J. Mass Spectrom. 174:95-100.
45. Paizs B, Schnoelzer M,Warnken U, Suhai S, Harrison AG (2004): Cleavage of the amide bond of protonated dipeptides. Phys. Chem. Chem. Phys. 6:2691-2699.
46. Paizs B, Suhai S (2005): Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24:508-548.
47. Paizs B, Suhai S (2004): Towards understanding the tandem mass spectra of protonated oligopeptides. 1: Mechanism of amide bond cleavage. J. Am. Soc. Mass Spectrom. 15:103-113.
48. Payne AH, Glish GL (2001): Thermally assisted infrared multiphton photodissociation in a quadrupole ion trap. Anal. Chem. 73:3542-3548.
49. Polfer NC, Oomens J, Suhai S, Paizs B (2005): Spectroscopic and theoretical evidence for oxazolone ring formation in collision-induced dissociation of peptides. J. Am. Chem. Soc. 127:17154-17155
50. Price WD, Schnier PD,Williams ER (1996.):Tandem mass spectrometry of large biomolecule ions by blackbody infrared radiative dissociation. Anal. Chem. 68:859-866.
51. Reid GE, Simpson RJ, O'Hair RAJ (2000): Leaving group and gas phase neighboring group effects in the side chain losses from protonated serine and its derivatives. J. Am. Soc. Mass Spectrom. 11:1047-1060.
52. Resing KA, Meyer-Arendt K, Mendoza AM, Aveline-Wolf LD, Jonscher KR, Pierce KG, Old WM, Cheung HT, Russell S, Wattawa JL, Goehle GR, Knight RD, Ahn NG (2004): Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem. 76:3556-3568.
53. Reynolds KJ, Yao X, Fenselau C (2002): Proteolytic 18O labeling for comparative proteomics: Evaluation of endoprotease glu-C as the catalytic agent. J. Proteome Res. 1:27-33.
54. Rodriquez CF, Cunje A, Shoeib T, Chu IK, Hopkinson AC, Siu KW (2001): Proton migration and tautomerism in protonated triglycine. J. Am. Chem. Soc. 123:3006-3012.
55. Roepstorff P (1984): Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11:601.
56. Sadagopan N,Watson JT (2001): Mass spectrometric evidence for mechanisms of fragmentation of charge-derivatized peptides. J. Am. Soc. Mass Spectrom. 12:399-409.
57. Schnier P, PriceW, Jockusch R,Williams E (1996): Blackbody infrared radiative dissociation of bradykinin and its analogues: Energetics, dynamics, and evidence for salt-bridge structures in the gas phase. J. Am. Chem. Soc. 118:7178-7189.
58. Somogyi A, Wysocki VH, Mayer I (1994): The effect of protonation site on bond strengths in simple peptides: Application of ab initio and modified neglect of differential overlap bond orders and modified neglect of differential overlap energy partitioning. J. Am. Soc. Mass Spectrom. 5:704-717.
59. Stimson E, Truong O, Richter WJ, Waterfield MD, Burlingame AL (1997): Enhancementof charge remote fragmentation in protonated peptides by high-energy CID MALDI-TOF-MS using "cold" matrices. Int. J. Mass Spectrom. 169:231-240.
60. Summerfield SG, Cox KA, Gaskell SJ (1997): The promotion of d-type ions during the low energy collision-induced dissociation of some cysteic acid-containing peptides. J. Am. Soc. Mass Spectrom. 8:25-31.
61. Summerfield SG, Steen H, O'Malley M, Gaskell SJ (1999): Phenyl thiocarbamoyl and related derivatives of peptides: Edman chemistry in the gas phase. Int. J. Mass Spectrom. 188:95-103.
62. Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004): Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 101:9528-9533.
63. Tabb DL, Huang Y, Wysocki VH, Yates JR, III (2004): Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76:1243-1248.
64. Tabb DL, Smith LL, Breci LA, Wysocki VH, Lin D, Yates JR, III (2003): Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal. Chem. 75:1155-1163.
65. Thompson MS, Cui W, Reilly JP (2004): Mass spectrometry: Fragmentation of singly charged peptide ions by photodissociation at l = 157 nm. Angew. Chem. Int. Ed. 43:4791- 4794.
66. Tsang CW, Harrison AG (1976): Chemical ionization of amino-acids. J. Am. Chem. Soc. 98:1301-1308.
67. Tsaprailis G, Nair H, ZhongW, Kuppannan K, Futrell JH,Wysocki VH (2004): A mechanistic investigation of the enhanced cleavage at histidine in the gas-phase dissociation of protonated peptides. Anal. Chem. 76:2083-2094.
68. van Dongen WD, Ruijters HF, Luinge HJ, Heerma W, Haverkamp J (1996): Statistical analysis of mass spectral data obtained from singly protonated peptides under high-energy collision-induced dissociation conditions. J. Mass Spectrom. 31:1156- 1162.
69. Wee S, O'Hair RAJ, McFadyen WD (2002): Side-chain radical losses from radical cations allows distinction of leucine and isoleucine residues in the isomeric peptides Gly-XXXArg. Rapid Commun. Mass Spectrom. 16:884-890.
70. Wu J, Lebrilla CB (1995): Intrinsic basicity of oligomeric peptides that contain glycine, alanine, and valine-the effects of the alkyl side chain on proton transfer reactions. J. Am. Soc. Mass Spectrom. 6:91-101.
71. Wysocki VH, Breci L, Hermann K (no date): Unpublished results.
72. Wysocki VH, Tsaprailis G, Smith LL, Breci LA (2000): Mobile and localized protons: A framework for understanding peptide dissociation. J. Mass Spectrom. 35:1399-1406.
73. Wyttenbach T, Bowers MT (1999): Gas phase conformations of biological molecules: The hydrogen/deuterium exchange mechanism. J. Am. Soc. Mass Spectrom. 10:9-14.
74. Yalcin T, Csizmadia IG, Peterson MR, Harrison AG (1996): The structure and fragmentation of Bn (n >= 3) ions in peptide spectra. J. Am. Soc. Mass Spectrom. 7:233-242.
75. Yalcin T, Khouw C, Csizmadia IG, Peterson MR, Harrison AG (1995): Why are B ions stable species in peptide spectra? J. Am. Soc. Mass Spectrom. 6:1165-1174.
76. Zhang J, Schubothe K, Li B, Russell S, Lebrilla CB (2005): Infrared multiphoton dissociation of O-linked mucin-type oligosaccharides. Anal. Chem. 77:208-214.
77. Zhang Q, Wysocki VH (no date): Unpublished results.
78. Zhang Z (2004): Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76:3908-3922.
79. Zubarev RA, Haselmann KF, Budnik B, Kjeldsen F, Jensen F (2002): Towards an understanding of the mechanism of electron-capture dissociation: A historical perspective and modern ideas. Eur. J. Mass Spetrom. 8:337-349.
80. Zubarev RA, Kelleher NL, McLafferty FW (1998): Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 120:3265-3266.