Gas-phase conformations of small polyprolines and their fragment ions by IRMPD spectroscopy

International Journal of Mass Spectrometry

Volumn 377, Issue 1, 2015, Pages 179-187

  Martens, Jonathan K ^a   Grzetic, Josipa ^a   Berden, Giel ^a   Oomens, Jos ^a,b  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

Diketopiperazine b2+; Ion spectroscopy; IRMPD; Peptide fragmentation; Polyproline; Proline effect

Indexed keywords

EID: 85027955309     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2014.07.027     Document Type: Article

References (53)

1. Y. Huang, G. C. Tseng, S. Yuan, L. Pasa-Tolic, M. S. Lipton, R. D. Smith, V. H. Wysocki, A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns, J. Proteome Res. 7 (1) (2007) 70-79.
2. W. Li, L. Ji, J. Goya, G. Tan, V. H. Wysocki, An intensity-incorporated protein identification algorithm for tandem mass spectrometry, J. Proteome Res. 10 (4) (2011) 1593-1602.
3. V. H. Wysocki, G. Tsaprailis, L. L. Smith, L. A. Breci, Mobile and localized protons: a framework for understanding peptide dissociation, J. Mass Spectrom. 35 (12) (2000) 1399-1406.
4. B. Paizs, S. Suhai, Fragmentation pathways of protonated peptides, Mass Spectrom. Rev. 24 (4) (2005) 508-548.
5. K. A. Cox, S. J. Gaskell, M. Morris, A. Whiting, Role of the site of protonation in the low-energy decompositions of gas-phase peptide ions, J. Am. Soc. Mass Spectrom. 7 (6) (1996) 522-531.
6. R. Boyd, Somogyi Á, The mobile proton hypothesis in fragmentation of protonated peptides: a perspective, J. Am. Soc. for Mass Spectrom. 21 (8) (2010) 1275-1278.
7. A. R. Dongré, J. L. Jones, Á Somogyi, V. H. Wysocki, Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model, J. Am. Chem. Soc. 118 (35) (1996) 8365-8374.
8. B. Paizs, S. Suhai, Towards understanding the tandem mass spectra of protonated oligopeptides. 1: mechanism of amide bond cleavage, J. Am. Soc. Mass Spectrom. 15 (1) (2004) 103-113.
9. T. Yalcin, C. Khouw, I. G. Csizmadia, M. R. Peterson, A. G. Harrison, Why are B ions stable species in peptide spectra? J. Am. Soc. Mass Spectrom. 6 (12) (1995) 1165-1174.
10. T. Yalcin, I. G. Csizmadia, M. R. Peterson, A. G. Harrison, The structure and fragmentation of Bn (n> 3) ions in peptide spectra, J. Am. Soc. Mass Spectrom. 7 (3) (1996) 233-242.
11. 2 ions in peptide mass spectra, J. Am. Soc. Mass Spectrom. 11 (5) (2000) 427-436.
12. B. Paizs, S. Suhai, Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. I. Cis-trans isomerization around protonated amide bonds, Rapid Commun. Mass Spectrom. 15 (23) (2001) 2307-2323.
13. B. Paizs, S. Suhai, Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. II. Formation of b2, y1, and y2 ions, Rapid Commun. Mass Spectrom. 16 (5) (2002) 375-389.
14. 2+ ion formation for histidine analogue-containing peptides, J. Phys. Chem. A 116 (17) (2012) 4296-4304.
15. 2+ ion, J. Am. Chem. Soc. 131 (48) (2009) 17528-17529.
16. D. Pal, P. Chakrabarti, Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations, J. Mol. Biol. 294 (1) (1999) 271-288.
17. A. Jabs, M. S. Weiss, R. Hilgenfeld, Non-proline cis peptide bonds in proteins, J. Mol. Biol. 286 (1) (1999) 291-304.
18. M. J. Nold, B. A. Cerda, C. Wesdemiotis, Proton affinities of the N- and C-terminal segments arising upon the dissociation of the amide bond in protonated peptides, J. Am. Soc. Mass Spectrom. 10 (1) (1999) 1-8.
19. J. F. Brandts, M. Brennan, L.-N. Lin, Unfolding and refolding occur much faster for a proline-free proteins than for most proline-containing proteins, Proc. Natl. Acad. Sci. 74 (10) (1977) 4178-4181.
20. C. Bleiholder, S. Suhai, A. Harrison, B. Paizs, Towards understanding the tandem mass spectra of protonated oligopeptides. 2: the proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala-Ser-Leu-Val-PheandTrp), J. Am. Soc. Mass Spectrom. 22 (6) (2011) 1032-1039.
21. L. A. Breci, D. L. Tabb, J. R. Yates, V. H. Wysocki, Cleavage N-terminal to proline; analysis of a database of peptide tandem mass spectra, Anal. Chem. 75 (9) (2003) 1963-1971.
22. R. N. Grewal, H. El Aribi, A. G. Harrison, K. W. M. Siu, A. C. Hopkinson, Fragmentation of protonated tripeptides: the proline effect revisited, J. Phys. Chem. B 108 (15) (2004) 4899-4908.
23. A. G. Harrison, A. B. Young, Fragmentation reactions of deprotonated peptides containing proline. The proline effect, J. Mass Spectrom. 40 (9) (2005) 1173-1186.
24. B. L. Schwartz, M. M. Bursey, Some proline substituent effects in the tandem mass spectrum of protonated pentaalanine, Biol. Mass Spectrom. 21 (2) (1992) 92-96.
25. T. Vaisar, J. Urban, Probing proline effect in CID of protonated peptides, J. Mass Spectrom. 31 (10) (1996) 1185-1187.
26. J. A. Loo, C. G. Edmonds, R. D. Smith, Tandem mass spectrometry of very large molecules. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization, Anal. Chem. 65 (4) (1993) 425-438.
27. D. F. Hunt, J. R. Yates, J. Shabanowitz, S. Winston, C. R. Hauer, Protein sequencing by tandem mass spectrometry, Proc. Natl. Acad. Sci. 83 (17) (1986) 6233-6237.
28. S. A. Martin, K. Biemann, A comparison of keV atom bombardment mass spectra of peptides obtained with a two-sector mass spectrometer with those from a four-sector tandem mass spectrometer, Int. J. Mass Spectrom. Ion Process. 78 (0) (1987) 213-228.
29. X. J. Tang, P. Thibault, R. K. Boyd, Fragmentation reactions of multiplyprotonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation, Anal. Chem. 65 (20) (1993) 2824-2834.
30. T. Vaisar, J. Urban, Gas-phase fragmentation of protonated mono-N-methylated peptides. Analogy with solution-phase acid-catalyzed hydrolysis, J. Mass Spectrom. 33 (6) (1998) 505-524.
31. E. A. Kapp, F. Schütz, G. E. Reid, J. S. Eddes, R. L. Moritz, R. A. J. O'Hair, T. P. Speed, R. J. Simpson, Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation, Anal. Chem. 75 (22) (2003) 6251-6264.
32. A. G. Unnithan, M. J. Myer, C. J. Veale, A. S. Danell, MS/MS of protonated polyproline peptides: the influence of N-terminal protonation on dissociation, J. Am. Soc. Mass Spectrom. 18 (12) (2007) 2198-2203.
33. M. Moradi, V. Babin, C. Roland, T. A. Darden, C. Sagui, Conformations and free energy landscapes of polyproline peptides, Proc. Natl. Acad. Sci. 106 (49) (2009) 20746-20751.
34. A. E. Counterman, D. E. Clemmer, Anhydrous polyproline helices and globules, J. Phys. Chem. B 108 (15) (2004) 4885-4898.
35. 2 fragment ion from protonated tri-alanine, J. Am. Soc. for Mass Spectrom. 20 (2) (2009) 334-339.
36. 4 fragment ions of protonated pentapeptides in the XH (XC, N, O) region, J. Phys. Chem. A 117 (12) (2013) 2508-2516.
37. + ion, J. Am. Chem. Soc. 130 (52) (2008) 17644-17645.
38. 2-ions from peptides containing Gln and Asn residues, J. Am. Soc. Mass Spectrom. 24 (8) (2013) 1228-1241.
39. J. J. Valle, J. R. Eyler, J. Oomens, D. T. Moore, A. F. G. Van Der Meer, G. Von Helden, G. Meijer, C. L. Hendrickson, A. G. Marshall, G. T. Blakney, Free electron laser-Fourier transform ion cyclotron resonance mass spectrometry facility for obtaining infrared multiphoton dissociation spectra of gaseous ions, Rev. Sci. Instrum. 76 (2) (2005) 23103.
40. A. Friedrich, M. Jainta, M. Nieger, S. Bräse, One-Pot synthesis of symmetrical and unsymmetrical diketopiperazines from unprotected amino acids, Synlett. 2007, (2007) 2127-2129 (EFirst).
41. D. A. Case T. A D, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Goetz, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. X. Cai Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, P. A. Kollman, AMBER, University of California, San Francisco, 2012.
42. C. N. Stedwell, J. F. Galindo, K. Gulyuz, A. E. Roitberg, N. C. Polfer, Crown complexation of protonated amino acids: influence on IRMPD spectra, J. Phys. Chem. A 117 (6) (2012) 1181-1188.
43. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, A. Robbm, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2009.
44. C. Bleiholder, S. Suhai, B. Paizs, Revising the proton affinity scale of the naturally occurring α-amino acids, J. Am. Soc. Mass Spectrom. 17 (9) (2006) 1275-1281.
45. A. G. Harrison, The gas-phase basicities and proton affinities of amino acids and peptides, Mass Spectrom. Rev. 16 (4) (1997) 201-217.
46. S. Gronert, D. C. Simpson, K. M. Conner, A reevaluation of computed proton affinities for the common α-amino acids, J. Am. Soc. Mass Spectrom. 20 (11) (2009) 2116-2123.
47. T. C. Dinadayalane, G. N. Sastry, J. Leszczynski, Comprehensive theoretical study towards the accurate proton affinity values of naturally occurring-amino acids, Int. J. Quantum Chem. 106 (14) (2006) 2920-2933.
48. E. P. L. Hunter, S. G. Lias, Evaluated gas phase basicities and proton affinities of molecules: an update, J. Phys. Chem. Ref. Data 27 (3) (1998) 413-656.
49. + with the proline amino acid. Complexation modes, potential energy profiles, and metal ion affinities, J. Phys. Chem. B 107 (11) (2003) 2588-2594.
50. E. J. Milner-White, L. H. Bell, P. H. Maccallum, Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides: different puckers are favoured in certain situations, J. Mol. Biol. 228 (3) (1992) 725-734.
51. + protonated peptide, Int. J. Mass Spectrom. 308 (2-3) (2011) 281-288.
52. A. Cimas, T. D. Vaden, T. S. J. A. De Boer, L. C. Snoek, M. P. Gaigeot, Vibrational spectra of small protonated peptides from finite temperature MD simulations and IRMPD spectroscopy, J. Chem. Theory Comput. 5 (4) (2009) 1068-1078.
53. C. M. Leavitt, A. F. De Blase, C. J. Johnson, M. Van Stipdonk, A. B. McCoy, M. A. Johnson, Hiding in plain sight: unmasking the diffuse spectral signatures of the protonated N-terminus in isolated dipeptides cooled in a cryogenic ion trap, J. Phys. Chem. Lett. 4 (20) (2013) 3450-3457.