Negative ion fragmentations of disulfide-containing crosslinking reagents are competitive with aspartic acid side-chain-induced cleavages

Rapid Communications in Mass Spectrometry

Volumn 27, Issue 1, 2013, Pages 238-248

  Calabrese, Antonio N ^a   Wang, Tianfang ^a,b   Bowie, John H ^a   Pukala, Tara L ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b UNIVERSITY OF THE SUNSHINE COAST   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHAINS; CROSSLINKING; PEPTIDES; SULFUR COMPOUNDS;

ARM LENGTHS; ASPARTIC ACIDS; CROSS-LINKING REAGENTS; CROSSLINKER; ION FRAGMENTATION; LOWER ENERGIES; METHYLENE GROUPS; SIDE-CHAINS; SPACER ARMS; SPECTRA'S;

NEGATIVE IONS;

EID: 84871330896     PISSN: 09514198     EISSN: 10970231     Source Type: Journal    
DOI: 10.1002/rcm.6445     Document Type: Article

References (45)

1. A. Sinz,. Investigation of proteinprotein interactions in living cells by chemical crosslinking and mass spectrometry. Anal. Bioanal. Chem. 2010, 397, 3433.
2. A. Sinz,. Chemical crosslinking and mass spectrometry to map threedimensional protein structures and proteinprotein interactions. Mass Spectrom. Rev. 2006, 25, 663.
3. A. Leitner, T. Walzthoeni, A. Kahraman, F. Herzog, O. Rinner, M. Beck, R. Aebersold,. Probing native protein structures by chemical crosslinking, mass spectrometry, and bioinformatics. Mol. Cell. Proteomics 2010, 9, 1634.
4. J. Rappsilber,. The beginning of a beautiful friendship: crosslinking/mass spectrometry and modelling of proteins and multiprotein complexes. J. Struct. Biol. 2011, 173, 530.
5. E. V. Petrotchenko, C. H. Borchers,. Crosslinking combined with mass spectrometry for structural proteomics. Mass Spectrom. Rev. 2010, 29, 862.
6. A. Maiolica, D. Cittaro, D. Borsotti, L. Sennels, C. Ciferri, C. Tarricone, A. Musacchio, J. Rappsilber,. Structural analysis of multiprotein complexes by crosslinking, mass spectrometry, and database searching. Mol. Cell. Proteomics 2007, 6, 2200.
7. A. Sinz, S. Kalkhof, C. Ihling,. Mapping protein interfaces by a trifunctional cross-linker combined with MALDITOF and ESIFTICR mass spectrometry. J. Am. Soc. Mass Spectrom. 2005, 16, 1921.
8. G. B. Hurst, T. K. Lankford, S. J. Kennel,. Mass spectrometric detection of affinity purified crosslinked peptides. J. Am. Soc. Mass Spectrom. 2004, 15, 832.
9. M. A. Nessen, G. Kramer, J. Back, J. M. Baskin, L. E. Smeenk, L. J. de Koning, J. H. van Maarseveen, L. de Jong, C. R. Bertozzi, H. Hiemstra, C. G. de Koster,. Selective enrichment of azidecontaining peptides from complex mixtures. J. Proteome Res. 2009, 8, 3702.
10. P. T. Kasper, J. W. Back, M. Vitale, A. F. Hartog, W. Roseboom, L. J. de Koning, J. H. van Maarseveen, A. O. Muijsers, C. G. de Koster, L. de Jong,. An aptly positioned azido group in the spacer of a protein cross-linker for facile mapping of lysines in close proximity. ChemBioChem 2007, 8, 1281.
11. S. M. Chowdhury, X. Du, N. Tolic, S. Wu, R. J. Moore, M. U. Mayer, R. D. Smith, J. N. Adkins,. Identification of crosslinked peptides after clickbased enrichment using sequential collisioninduced dissociation and electron transfer dissociation tandem mass spectrometry. Anal. Chem. 2009, 81, 5524.
12. X. Tang, G. R. Munske, W. F. Siems, J. E. Bruce,. Mass spectrometry identifiable crosslinking strategy for studying proteinprotein interactions. Anal. Chem. 2005, 77, 311.
13. M. TresterZedlitz, K. Kamada, S. K. Burley, D. Fenyo, B. T. Chait, T. W. Muir,. A modular crosslinking approach for exploring protein interactions. J. Am. Chem. Soc. 2003, 125, 2416.
14. F. Chu, S. Mahrus, C. S. Craik, A. L. Burlingame,. Isotopecoded and affinitytagged crosslinking (ICATXL): an efficient strategy to probe protein interaction surfaces. J. Am. Chem. Soc. 2006, 128, 10362.
15. T. Taverner, N. E. Hall, R. A. O'Hair, R. J. Simpson,. Characterization of an antagonist interleukin6 dimer by stable isotope labeling, crosslinking, and mass spectrometry. J. Biol. Chem. 2002, 277, 46487.
16. E. V. Petrotchenko, V. K. Olkhovik, C. H. Borchers,. Isotopically coded cleavable cross-linker for studying proteinprotein interaction and protein complexes. Mol. Cell. Proteomics 2005, 4, 1167.
17. 18O labeling. Anal. Chem. 2002, 74, 4417.
18. D. M. Schulz, S. Kalkhof, A. Schmidt, C. Ihling, C. Stingl, K. Mechtler, O. Zschornig, A. Sinz,. Annexin A2/P11 interaction: new insights into annexin A2 tetramer structure by chemical crosslinking, highresolution mass spectrometry, and computational modeling. Proteins 2007, 69, 254.
19. C. Ihling, A. Schmidt, S. Kalkhof, D. M. Schulz, C. Stingl, K. Mechtler, M. Haack, A. G. BeckSickinger, D. M. Cooper, A. Sinz,. Isotopelabeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex. J. Am. Soc. Mass Spectrom. 2006, 17, 1100.
20. M. Q. Muller, F. Dreiocker, C. H. Ihling, M. Schafer, A. Sinz,. Cleavable crosslinker for protein structure analysis: reliable identification of crosslinking products by tandem MS. Anal. Chem. 2010, 82, 6958.
21. A. Kao, C. L. Chiu, D. Vellucci, Y. Yang, V. R. Patel, S. Guan, A. Randall, P. Baldi, S. D. Rychnovsky, L. Huang,. Development of a novel crosslinking strategy for fast and accurate identification of crosslinked peptides of protein complexes. Mol. Cell. Proteomics 2011, 10.
22. J. W. Back, A. F. Hartog, H. L. Dekker, A. O. Muijsers, L. J. de Koning, L. de Jong,. A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes. J. Am. Soc. Mass Spectrom. 2001, 12, 222.
23. E. J. Soderblom, M. B. Goshe,. Collisioninduced dissociative chemical crosslinking reagents and methodology: Applications to protein structural characterization using tandem mass spectrometry analysis. Anal. Chem. 2006, 78, 8059.
24. E. J. Soderblom, B. G. Bobay, J. Cavanagh, M. B. Goshe,. Tandem mass spectrometry acquisition approaches to enhance identification of proteinprotein interactions using lowenergy collisioninduced dissociative chemical crosslinking reagents. Rapid Commun. Mass Spectrom. 2007, 21, 3395.
25. G. J. King, A. Jones, B. Kobe, T. Huber, D. Mouradov, D. A. Hume, I. L. Ross,. Identification of disulfidecontaining chemical crosslinks in proteins using MALDITOF/TOFmass spectrometry. Anal. Chem. 2008, 80, 5036.
26. Y. Lu, M. Tanasova, B. Borhan, G. E. Reid,. Ionic reagent for controlling the gasphase fragmentation reactions of crosslinked peptides. Anal. Chem. 2008, 80, 9279.
27. M. W. Gardner, L. A. Vasicek, S. Shabbir, E. V. Anslyn, J. S. Brodbelt,. Chromogenic crosslinker for the characterization of protein structure by infrared multiphoton dissociation mass spectrometry. Anal. Chem. 2008, 80, 4807.
28. A. N. Calabrese, N. J. Good, T. Wang, J. He, J. H. Bowie, T. L. Pukala,. A negative ion mass spectrometry approach to identify crosslinked peptides using characteristic disulfide fragmentations. J. Am. Soc. Mass Spectrom. 2012, 23, 1364.
29. D. Bilusich, J. H. Bowie,. Identification of intermolecular disulfide linkages in underivatised peptides using negative ion electrospray mass spectrometry. A joint experimental and theoretical study. Rapid Commun. Mass Spectrom. 2007, 21, 619.
30. - anions of underivatised peptides. Part 2: Characteristic cleavages of Ser and Cys and of disulfides and other posttranslational modifications, together with some unusual internal processes. Mass Spectrom. Rev. 2009, 28, 20.
31. H. J. Andreazza, J. H. Bowie,. The application of negative ion electrospray mass spectrometry for the sequencing of underivatized disulfidecontaining proteins: insulin and lysozyme. Phys. Chem. Chem. Phys. 2010, 12, 13400.
32. D. Bilusich, V. M. Maselli, C. S. Brinkworth, T. Samguina, A. T. Lebedev, J. H. Bowie,. Direct identification of intramolecular disulfide links in peptides using negative ion electrospray mass spectra of underivatised peptides. A joint experimental and theoretical study. Rapid Commun. Mass Spectrom. 2005, 19, 3063.
33. M. Zhang, I. A. Kaltashov,. Mapping of protein disulfide bonds using negative ion fragmentation with a broadband precursor selection. Anal. Chem. 2006, 78, 4820.
34. - parent anions of underivatized peptides: an aid to structure determination and some unusual negative ion cleavages. Mass Spectrom. Rev. 2002, 21, 87.
35. S. Kalkhof, A. Sinz,. Chances and pitfalls of chemical crosslinking with aminereactive Nhydroxysuccinimide esters. Anal. Bioanal. Chem. 2008, 392, 305.
36. D. Vellucci, A. Kao, R. M. Kaake, S. D. Rychnovsky, L. Huang,. Selective enrichment and identification of azidetagged crosslinked peptides using chemical ligation and mass spectrometry. J. Am. Soc. Mass Spectrom. 2010, 21, 1432.
37. A. D. Becke,. Densityfunctional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648.
38. T. Yanai, D. P. Tew, N. C. Handy,. A new hybrid exchangecorrelation functional using the Coulombattenuating method (CAMB3LYP). Chem. Phys. Lett. 2004, 393, 51.
39. P. J. Stephens, F. J. Devlin, C. F. Chabalowski, M. J. Frisch,. Abinitio calculation of vibrational absorption and circulardichroism spectra using densityfunctional forcefields. J. Phys. Chem. 1994, 98, 11623.
40. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, 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. 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, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09, Revision B.01, Gaussian, Inc., Wallingford, CT, 2009.
41. K. Fukui,. The path of chemicalreactions-the IRC approach. Acc. Chem. Res. 1981, 14, 363.
42. C. Gonzalez, H. B. Schlegel,. An improved algorithm for reactionpath following. J. Chem. Phys. 1989, 90, 2154.
43. C. Gonzalez, H. B. Schlegel,. Reactionpath following in massweighted internal coordinates. J. Phys. Chem. 1990, 94, 5523.
44. R. J. Waugh, J. H. Bowie, R. N. Hayes,. Collisioninduced dissociations of deprotonated peptides. Dipeptides containing aspartic or glutamic acids. Org. Mass Spectrom. 1991, 26, 250.
45. - anions of peptides. New backbone cleavages following cyclisation of a Cterminal CONH group with Ser. Eur. J. Mass Spectrom. 2002, 8, 53.