To b or not to b: The ongoing saga of peptide b ions

Mass Spectrometry Reviews

Volumn 28, Issue 4, 2009, Pages 640-654

  Harrison, Alex G ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

B ion cyclization; B ions; Formation mechanisms; Fragmentation mechanisms; Oxazolones

Indexed keywords

B ION CYCLIZATION; B IONS; FORMATION MECHANISMS; FRAGMENTATION MECHANISMS; OXAZOLONES;

AMIDES; AMINATION; AMINES; AMINO ACIDS; CYCLIZATION; ORGANIC ACIDS; PEPTIDES;

IONS;

ION; OXAZOLONE; PEPTIDE; PROTON;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CYCLIZATION; ELECTROSPRAY MASS SPECTROMETRY; MASS SPECTROMETRY; METHODOLOGY;

CYCLIZATION; IONS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; OXAZOLONE; PEPTIDES; PROTONS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 68849096511     PISSN: 02777037     EISSN: None     Source Type: Journal    
DOI: 10.1002/mas.20228     Document Type: Article

References (82)

1. Aebersold R, Goodlett DR. 2001. Mass spectrometry in proteomics. Chem Rev 101:269-295.
2. Allen JM, Racine AH, Johnson JS, Bythell BJ, Paizs B, Glish GL. 2008. Why are a3 ions rarely observed? J Am Soc Mass Spectrom 19:1764-1770.
3. 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.
4. Arnott D, Kottmeir D, Yates N, Shabanowitz J, Hunt DF. 1994. Fragmentation of multiply protonated peptides under low energy conditions. Proc. 42nd ASMS Conference. Chicago, p. 470.
5. Barber M, Bordoli RS, Sedgwick RD, Tyler AN. 1981. Fast atom bombardment of solids (F. A. B.) : A new ion source for mass spectrometry. J Chem Soc Chem Commun 324-327.
6. Biemann K. 1988. Contribution of mass spectrometry to peptide and protein structure. Biomed Env Mass Spectrom 16:99-111.
7. Bleiholder C, Osburn S, Williams TD, Suhai S, Van Stipdonk M, Harrison AG, Paizs B. 2008. Sequence scrambling fragmentation pathways of protonated peptides. J Am Chem Soc 130:17774-17789.
8. Bouchoux G, Bourcier S, Hoppilliard Y, Mauriac C. 1993. Leucine and isoleucine in chemical ionization and plasma desorption mass spectrometry: A comparative study. Org Mass Spectrom 28:1064-1072.
9. Busch KL, Glish GL, McLuckey SA. 1988. Mass spectrometry/mass spectrometry: Techniques and applications of tandem mass spectrometry. New York: VCH.
10. 2 ions derived from deprotonated peptides." A comparison of method and basis set used on relative product stabilities. J Mol Struct (Theochem) 675:149-162.
11. Chen X, Turecek F. 2005. Simple b ions have cyclic oxazolone structures. A neutralization-reionization and computational study of oxazolone radicals. J Am Soc Mass Spectrom 16:1941-1956.
12. Cordero MM, Houser JJ, Wesdemiotis C. 1993. The neutral products formed during backbone fragmentation of protonated peptides in tandem mass spectrometry. Anal Chem 65:1594-1601.
13. 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.
14. Csonka IP, Paizs B, Lendvay G, Suhai S. 2001. Proton mobility and main fragmentation pathways of protonated lysylglycine. Rapid Commun Mass Spectrom 15:1457-1472. (Pubitemid 32786414)
15. Dongré 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.
16. Eckart K. 1994. Mass spectrometry of cyclic peptides. Mass Spectrom Rev 13:23-55.
17. 2 ions and their specifically deuterated analogues. J Am Soc Mass Spectrom 9:1002-1011.
18. El Aribi H, Rodriquez CF, Almeida DRF, Ling Y, Mak WW-N, Hopkinson AC, Siu KWM. 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.
19. Fang D-C, Yalcin T, Tang T-H, Fu X-Y, Harrison AG, Csizmadia IG. 1999. Electron distribution in cationic fragments generated mass spectrometrically from peptides. J Mol Struct (Theochem) 468:135-149.
20. 2 ions have oxazolone structures? Multistage mass spectrometry and ab initio studies on protonated N-acetyl amino acid methyl ester model systems. Int J Mass Spectrom 210/211: 71-87.
21. Farrugia JM, Taverner T, O'Hair RAJ. 2001. Side-chain involvement in the fragmentation reactions of the protonated methyl esters of histidine and its peptides. Int J Mass Spectrom 209:99-112.
22. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. 1989. Electrospray ionization mass spectrometry of large molecules. Science 246:64-71.
23. 1-1 product ions in the mass spectra of N-{para-(ferrocenyl) benzoyl}dipeptide esters. Rapid Commun Mass Spectrom 22:2398-2401.
24. Greenberg A, Hsing H-J, Liebman JF. 1995. Aziridinone and 2-azetidine and their protonated structures. An ab initio molecular orbital study making comparisons with bridgehead bicyclic lactones and acetamide. J Mol Struct (Theochem) 338:83-100.
25. Grewal RN, El Aribi H, Harrison AG, Siu KWM, Hopkinson AC. 2004. Fragmentation of protonated tripeptides: The proline effect revisited. J Phys Chem B 108:4899-4908.
26. Harrison AG. 1992. Chemical ionization mass spectrometry. 2nd edition. Boca Raton: CRC Press.
27. Harrison AG. 1999a. Linear free energy correlations in mass spectrometry. J Mass Spectrom 34:577-589.
28. Harrison AG. 1999b. Energy-resolved mass spectrometry: A comparison of quadrupole cell and cone-voltage collision-induced dissociation. Rapid Commun Mass Spectrom 13:1663-1670.
29. Harrison AG. 2008. Peptide sequence scrambling through cyclization of b5 ions. J Am Soc Mass Spectrom 19:1776-1780.
30. Harrison AG, Young AB. 2004. Fragmentation of protonated oligoalinines: Amide bond cleavage and beyond. JAm Soc Mass Spectrom 15:1810-1819.
31. 2 ions in peptide mass spectra. JAm Soc Mass Spectrom 11:427-436.
32. Harrison AG, Csizmadia IG, Tang T-H, Tu Y-P. 2000. Reaction competitionin the fragmentation of protonated dipeptides. J Mass Spectrom 35:683-688.
33. Harrison AG, Young AB, Bleiholder C, Suhai S, Paizs B. 2006. Scrambling of sequence information in collision-induced dissociation of peptides. J Am Chem Soc 128:10364-10365.
34. 2+ peptide fragments reveals the presence of the acylium ion structure. Rapid Commun Mass Spectrom 14:2242-2246.
35. 1-ions in the product ion spectra of dipeptides containing N-terminal basic amino acid residues. J Am Soc Mass Spectrom 18:1414-1422.
36. Holmes JL, Aubry C, Mayer PM. 2007. Assigning structures to ions in mass spectrometry. CRC Press: Boca Raton.
37. Jia C, Qi W, He Z. 2007. Cyclization reactionsofpeptide fragmentions during multistage collisionally activated decomposition: An inducement to lose internal amino acid residues. J Am Soc Mass Spectrom 18:663-678.
38. Karas M, Hillenkamp F. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10, 000 Da. Anal Chem 60:2299-2301.
39. McLuckey SA, Cooks RG. 1983. Angle-and energy-resolved fragmentation spectra from tandem mass spectrometry. In: McLafferty FW, editor. Tandem mass spectrometry. New York: Wiley. pp. 303-320.
40. Medzihradszky KF. 2005. Peptide sequence analysis. Methods Enzymol 402:209-244.
41. Meot-Ner M, Field FH. 1973. Chemical ionization mass spectrometry. XX Energy effects and virtual ion temperatures in the decomposition kinetics of amino acids and amino acid derivatives. J Am Chem Soc 95:7207-7211.
42. Milne GWA, Axenrod T, Fales HM. 1970. Chemical ionization mass spectrometry of complex molecules. IV. Amino acids. J Am Chem Soc 92:5170-5175.
43. Morgan DG, Bursey MM. 1994. A linear free energy correlation in the low energy tandem mass spectra of protonated tripeptides Gly-Gly-Xxx. Org Mass Spectrom 29:354-359.
44. Mouls L, Aubagnac J-L, Martinez J, Enjalbal C. 2007. Low energy peptide fragmentations in an ESI-Q-Tof mass spectrometer. J Proteome Res 6:1378-1391.
45. Mueller DR, Eckersley M, Richter W. 1988. Hydrogen transfer reactions in the formation of "Y + 2" sequence ions from protonated peptides. Org Mass Spectrom 23:213-232.
46. Ngoka LCM, Gross ML. 1999. A nomenclature system for labeling cyclic peptide fragments. J Am Soc Mass Spectrom 10:360-363.
47. Nold MJ, Wesdemiotis C, Yalcin T, Harrison AG. 1997. Amide bond dissociation in protonated peptides. Structures of the N-terminal ionic and neutral fragments. Int J Mass Spectrom Ion Process 164:137-153.
48. Paizs B, Suhai S. 2001. Combined quantumchemical and RRKM modeling of the main fragmentation pathways of protonated GGG. 1. Cis-trans isomerization around protonated amide bonds. Rapid Commun Mass Spectrom 15:2307-2323.
49. Paizs B, Suhai S. 2004. Towards understanding the tandem mass spectra of protonated oligopeptides. I. Mechanism of amide bond cleavage. J Am Soc Mass Spectrom 15:103-112.
50. Paizs B, Suhai S. 2005. Fragmentation pathways of protonated peptides. Mass Spectrom Rev 24:508-548.
51. 2 ions from protonated peptides: An abinitio study. Rapid Commun Mass Spectrom 13:525-533.
52. 2 ions of protonated peptides. An ab initio study. Rapid Commun Mass Spectrom 14:746-755. (Pubitemid 30351413)
53. Paizs B, Csonka IP, Lendvay G, Suhai S. 2001. Proton mobility in protonated glycylglycine and N-formylglycylglycinamide: A combined quantum chemical and RRKM study. Rapid Commun Mass Spectrom 15:637-650.
54. 2. Int J Mass Spectrom 219:203-232.
55. Polfer NC, Oomens J, Suhai S, Paizs B. 2005. Spectroscopic and theoretical evidence for oxazolone ring formationin collision-induced dissociation of peptides. J Am Chem Soc 127:17154-17155.
56. Polfer NC, Oomens J, Suhai S, Paizs B. 2007. Infrared spectroscopy and theoretical studies on gas-phase protonated Leu-enkephalin and its fragments: direct experimental evidence for the mobile proton. J Am Chem Soc 129:5887-5897.
57. Polfer NC, Bohrer BC, Plasencia MD, Paizs B, Clemmer DE. 2008. On the dynamics of fragment isomerization in collision-induced dissociation of peptides. J Phys Chem A 108:1286-1293.
58. + ions. J Am Soc Mass Spectrom 9:945-956.
59. Riba-Garcia I, Giles K, Bateman RH, Gaskell SJ. 2008. Evidence for structural variants of a-and b-type peptide fragment ions using combined ion mobility/mass spectrometry. J Am Soc Mass Spectrom 19:609-613.
60. + potential energy surfaces. J Mol Struct (Theochem) 401:117-125.
61. Rodriquez CF, Shoeib T, Chu IK, Siu KWM, Hopkinson AC. 2000. Comparison between protonation, lithiation and argentination of 5-oxazolones: A study of a key intermediate in gas-phase peptide sequencing. J Phys Chem A 104:5335-5342.
62. Roepstorff P, Fohlmann J. 1984. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11:601.
63. Savitski MM, Fath M, Fung YME, Adams CM, Zubarev RA. 2008. Bifurcating behaviour of gas-phase tryptic peptide dications in collisional activation. J Am Soc Mass Spectrom 19:1755-1763.
64. Smith LL, Hermann KA, Wysocki VH. 2006. Investigation of gas-phase structures for proline-containing b2 ions. J Am Soc Mass Spectrom 17:20-28.
65. 1 ions in peptide phenylthiocarbamoyl derivatives: Analogies with condensed-phase chemistry. J Mass Spectrom 32:225-231.
66. Tang X-J, Boyd RK. 1994. Rearrangement of doubly-charged acylium ions from lysyl and ornithyl peptides. Rapid Commun Mass Spectrom 8:678-686.
67. Tang X-J, Thibault P, Boyd RK. 1993. Fragmentation reactions of multiplyprotonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation. Anal Chem 65:2824-2834.
68. Tang T-H, Fang D-C, Harrison AG, Csizmadia IG. 2004. A computational study of the fragmentation of b3 ions derived from protonated peptides. J Mol Struct (Theochem) 675:79-93.
69. Tsang CW, Harrison AG. 1976. Chemical ionization of amino acids. J Am Chem Soc 98:1301-1308.
70. Tsaprailis G, Nair H, Zhang W, 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.
71. 1 ion derived from methionine is a stable species. Rapid Commun Mass Spectrom 12:849-851.
72. Vaisar T, Urban J. 1996. Probing the proline effect in CID of protonated peptides. J Mass Spectrom 31:1185-1187.
73. Vaisar T, Urban J. 1998. Gas-phase fragmentation of mono-N-methylated peptides. Analogy with solution-phase acid-catalyzed hydrolysis. J Mass Spectrom 33:505-524.
74. 2 and CO. Rapid Commun Mass Spectrom 10:1237-1239.
75. Wysocki VH, Tsaprailis G, Smith LL, Breci LA. 2000. Mobile and localized protons: A framework for understanding peptide fragmentation. J Mass Spectrom 35:1399-1406.
76. Yague J, Paradela A, Ramos M, Ogueta S, Marina A, Barahona F, Lopez de Castro JA, Vazquez J. 2003. Peptide rearrangement during ion trap fragmentation: Added complexity to MS/MS spectra. Anal Chem 75:1524-1535.
77. Yalcin T, Harrison AG. 1996. Ion chemistry of protonated lysine derivatives. J Mass Spectrom 31:1237-1243.
78. Yalcin T, Khouw C, Csizmadia IG, Peterson MR, Harrison AG. 1995. Why are B ions stable species in peptide mass spectra? J Am Soc Mass Spectrom 6:1165-1174.
79. n (n ≥ 3) ions in peptide spectra. J Am Soc Mass Spectrom 7:233-242.
80. Yalcin T, Gabryelski W, Li L. 1998. Dissociation of protonated phenylthiohydantoin-amino acids and phenylthiocarbamoyl-dipeptides. J Mass Spectrom 33:543-553.
81. Zhang L, Reilly JP. 2008. Use of 157-nmphotodissociation to probe structures of y-and b-type ions produced in collision-induced dissociation of peptide ions. J Am Soc Mass Spectrom 19:695-702.
82. 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.