Traveling-wave ion mobility mass spectrometry analysis of isomeric modified peptides arising from Chemical Cross-Linking

Journal of the American Society for Mass Spectrometry

Volumn 21, Issue 12, 2010, Pages 2062-2069

  Santos, Luiz F A ^a   Iglesias, Amadeu H ^a   Pilau, Eduardo J ^a   Gomes, Alexandre F ^a   Gozzo, Fabio C ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ARRIVAL-TIME DISTRIBUTIONS; CHEMICAL CROSS-LINKING; CONFORMATIONAL ANALYSIS; FRAGMENT IONS; INTRINSIC REACTIVITY; ION MOBILITY; ION MOBILITY-MASS SPECTROMETRY; PEPTIDE IONS; PH CONDITION; PRODUCT ION SPECTRA; SYNTHETIC PEPTIDE; TRAVELING WAVE;

CHEMICAL ANALYSIS; CHEMICAL MODIFICATION; CROSSLINKING; ISOMERS; MASS SPECTROMETRY; PEPTIDES;

IONS;

LYSINE; SYNTHETIC PEPTIDE;

ARTICLE; CONTROLLED STUDY; ION MOBILITY SPECTROMETRY; ISOMER; PEPTIDE ANALYSIS; PH; PROTEIN CROSS LINKING; PROTEIN DETERMINATION; PROTEIN MODIFICATION; SEPARATION TECHNIQUE; TRAVELING WAVE ION MOBILITY SPECTROMETRY;

AMINO ACID SEQUENCE; CROSS-LINKING REAGENTS; HYDROGEN-ION CONCENTRATION; ISOMERISM; LYSINE; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN CONFORMATION;

EID: 78649443024     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2010.08.017     Document Type: Article

References (70)

1. Gruis D.B., Price E.M. The Nucleotide Binding Folds of the Cystic Fibrosis Transmembrane Conductance Regulator are Extracellularly Accessible. Biochemistry 1997, 36:7739-7745.
2. Patchornik G. Purification of His-Tagged Proteins with [Desthiobiotin#BSA#EDTA] Conjugates Exhibiting Resistance to EDTA. Bioconj. Chem. 2008, 19:673-679.
3. Shell S.M., Hess S., Kvaratskhelia M., Zou Y. Mass Spectrometric Identification of Lysines Involved in the Interaction of Human Replication Protein A with Single-Stranded DNA. Biochemistry 2005, 44:971-978.
4. Ioffe M.V., Gorbenko G.P., Kinnunen P.K.J., Tatarets A.L., Kolosova O.S., Patsenker L.D., Terpetsching E.A. Tracing Lysozime-Lipid Interactions with Long-Wavelength Saquarine Dyes. J. Fluoresc. 2007, 17:65-72.
5. Fan J., Pope L.E., Vitols K.S., Huennekens F.M. Affinity Labeling of Folate Transport Proteins with the N-Hydroxysuccinimide Ester of γ-Isomer of Fluorescein-Methotrexate. Biochemistry 1991, 30:4573-4580.
6. Gabant G., Augier J., Armengaud J. Assessment of Solvent Residues Accessibility Using Three Sulfo-NHS-Biotin Reagents in Parallel: Application to Footprint Changes of a Methyltransferase Upon Binding Its Substrate. J. Mass Spectrom. 2008, 43:360-370.
7. Shkriabai N., Datta S.A.K., Zhao Z., Hess S., Rein A., Kvaratskhelia M. Interactions of HIV-1 Gag with Assembly Cofactors. Biochemistry 2006, 45:4077-4083.
8. Barnhill H.N., Reuther R., Ferguson P.L., Dreher T., Wang Q. Turnip Yellow Mosaic Virus as a Chemoaddressable Bionanoparticle. Bioconj. Chem. 2007, 18:852-859.
9. Back J.W., Jong L., Muijsers A.O., Koster C.G. Chemical Cross-Linking and Mass Spectrometry for Protein Structural Modeling. J. Mol. Biol. 2003, 331:303-313.
10. Sinz A. Chemical Cross-Linking and Mass Spectrometry to Map Three-Dimensional Protein Structures and Protein-Protein Interactions. Mass Spectrom. Rev. 2005, 25:663-682.
11. 35S] Dithiobis. J. Mol. Biol. 1976, 104:243-261. (succinimidyl propionate).
12. Chen Z.A., Jawhari A., Fischer L., Buchen C., Tahir S., Kamenski T., Rasmussen M., Lariviere L., Bukowski-Wills J.-C., Nilges M., Cramer P., Rappsilber J. Architecture of the RNA Polymerase II-TFIIF Complex Revealed By Cross-Linking and Mass Spectrometry. EMBO J. 2010, 29:717-726.
13. Tubb M.R., Silva R.A.G.D., Fang J., Tso P., Davidson W.S. A Three-Dimensional Homology Model of Lipid-free Apolipoprotein A-IV Using Cross-Linking and Mass Spectrometry. J. Biol. Chem. 2008, 283:17314-17323.
14. Hermanson G.T. Bioconjugate Techniques 2008, Academic Press, Elsevier Inc, San Diego, p. 171. 2nd ed.
15. Guo X., Bandyopadhyay P., Schilling B., Young M.M., Fujii N., Aynechi T., Guy R.K., Kuntz I.D., Gibson B.W. Partial Acetylation of Lysine Residues Improves Intraprotein Cross-linking. Anal. Chem. 2008, 80:951-960.
16. Madler S., Bich C., Touboul D., Zenobi R. Chemical Cross-Linking with NHS Esters: A Systematic Study on Amino Acid Reactivities. J. Mass Spectrom. 2009, 44:694-706.
17. Swaim C.L., Smith J.B., Smith D.L. Unexpected Products from the Reaction of the Synthetic Cross-Linker 3,3-Dithiobis(Sulfosuccinimidyl propionate), DTSSP with Peptides. J. Am. Soc. Mass Spectrom. 2004, 15:736-749.
18. Leavell M.D., Novak P., Behrens C.R., Schoeniger J.R., Kruppa G.H. Strategy for Selective Chemical Cross-linking of Tyrosine and Lysine Residues. J. Am. Soc. Mass Spectrom. 2004, 15:1604-1611.
19. Schilling B., Row R.H., Gibson B.W., Guo X., Young M.M. MS2Assign, Automated Assignment and Nomenclature of Tandem Mass Spectra of Chemically Cross-Linked Peptides. J. Am. Soc. Mass Spectrom. 2003, 14:834-850.
20. Lee Y.J. Mass Spectrometric Analysis of Cross-Linking Sites for the Structure of Proteins and Protein Complexes. Mol. BioSyst. 2008, 4:816-823.
21. Huang B.X., Kim H.Y., Dass C. Probing Three-Dimensional Structure of Bovine Serum Albumin by Chemical Cross-Linking and Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2004, 15:1237-1247.
22. Kalkhof S., Sinz A. Chances and Pitfalls of Chemical Cross-Linking with Amine-Reactive N-hydroxysuccinimide Esters. Anal. Bioanal. Chem. 2008, 392:305-312.
23. Pimenova T., Nazabal A., Roschitzki B., Seebacher J., Rinner O., Zenobi R. Epitope Mapping on Bovine Prion Protein Using Chemical Cross-Linking and Mass Spectrometry. J. Mass Spectrom. 2008, 43:185-195.
24. Iglesias A.H., Santos L.F.A., Gozzo F.C. Collision-Induced Dissociation of Lys-Lys Intramolecular Cross-Linked Peptides. J. Am. Soc. Mass Spectrom. 2009, 4:557-566.
25. Iglesias A.H., Santos L.F.A., Gozzo F.C. Identification of Cross-Linked Peptides by High-Resolution Precursor Ion Scan. Anal. Chem. 2010, 82:909-916.
26. King G.J., Jones A., Kobe B., Huber T., Mouradov D., Hume D.A., Ross I.L. Identification of Disulfide-Containing Chemical Cross-Links in Proteins Using MALDI-TOF/TOF-Mass Spectrometry. Anal. Chem. 2008, 80:5036-5043.
27. Kanu A.B., Dwivedi P., Tam M., Matz L., Hill H.H. Ion Mobility-Mass Spectrometry. J. Mass Spectrom. 2008, 43:1-22.
28. McDaniel E.W., Martin D.W., Barnes W.S. Drift-Tube Mass Spectrometer for Studies of Low-Energy Ion-Molecule reactions. Rev. Sci. Instrum. 1962, 33:2-7.
29. Albritton D.L., Miller T.M., Martin D.W., McDaniel E.W. Mobilities of Mass-Identified Ions in Hydrogen. Phys. Rev. 1968, 171:94-102.
30. McDaniel E.W. Possible Sources of Large Error in Determinations of Ion-Molecule Reaction Rates with Drift Tube-Mass Spectrometers. J. Chem. Phys. 1970, 52:3931-3935.
31. McAfee K.B., Sipler D.P., Edelson D. Mobilities and Reactions of Ions in Argon. Phys. Rev 1967, 160:130-135.
32. Edelson D., Morrison J.A., McKnight L.G., Sipler D.P. Interpretation of Ion-Mobility Experiments in Reacting Systems. Phys. Rev. 1967, 164:71-75.
33. Young C..E., Edelson D., Falconer W.E. Water Cluster Ions: Rates of Formation and Decomposition of Hydrates of the Hydronium Ion. J. Chem. Phys. 1970, 53:4295-4302.
34. Karasek F.W., Cohen M.J., Carroll D.I. Trace Studies of Alcohols in the Plasma Chromatography-Mass Spectrometer. J. Chromatogr. Sci. 1971, 9:390-392.
35. Kuk Y., Jarrold M.F., Silverman P.J., Bower J.E., Brown W.L. Preparation and Observation of Si10 clusters on a Au(001)-(5×20) Surface. Phys. Rev. B 1989, 39:11168-11170.
36. Kemper P.R., Bowers M.T. A Hybrid Double-Focusing Mass Spectrometer-High-Pressure Drift Reaction Cell to Study Thermal Energy Reactions of Mass-Selected Ions. J. Am. Soc. Mass Spectrom. 1990, 1:197-207.
37. Bowers M.T., Kemper P.R., von Helden G., Van Koppen P.A.M. Gas-Phase Ion Chromatography: Transition Metal State Selection and Carbon Cluster Formation. Science 1993, 260:1446-1451.
38. Gotts N.G., von Helden G., Bowers M.T. Carbon Cluster Anions: Structure and Growth from C5- to C62- Int. J. Mass Spectrom. Ion Processes 1995, 149:217-229.
39. Wyttenbach T., Witt M., Bowers M.T. On the Stability of Amino Acid Zwitterions in the Gas Phase: The Influence of Derivatization, Proton Affinity, and Alkali Ion Addition. J. Am. Chem. Soc. 2000, 122:3458-3464.
40. Srebalus C.A., Li J., Marshall W.S., Clemmer D.E. Gas-Phase Separations of Electrosprayed Peptide Libraries. Anal. Chem. 1999, 71:3918-3927.
41. Thalassinos K., Slade S.E., Jennings K.R., Scrivens J.H., Giles K., Wildgoose J., Hoyes J., Bateman R.H., Bowers M.T. Ion Mobility Mass Spectrometry of Proteins in a Modified Commercial Mass Spectrometer. Int. J. Mass Spectrom. 2004, 236:55-63.
42. Gidden J., Baker E.S., Ferzoco A., Bowers M.T. Structural Motifs of DNA Complexes in the Gas Phase. Int. J. Mass Spectrom. 2005, 240:183-193.
43. Gidden J., Wyttenbach T., Jackson A.T., Scrivens J.H., Bowers M.T. Gas-Phase Conformations of Synthetic Polymers: Poly(Ethylene Glycol), Poly(Propylene Glycol), and Poly(Tetramethylene glycol). J. Am. Chem. Soc. 2000, 122:4692-4699.
44. Kanu A.B., Dwivedi P., Tam M., Matz L., Hill H.H. Ion Mobility-Mass Spectrometry. J. Mass Spectrom. 2008, 43:1-22.
45. Purves R.W., Guevremont R., Day S., Pipich C.H., Matyjaszczyk M.S. Mass Spectrometric Characterization of a High-Field Asymmetric Waveform Ion Mobility Spectrometer. Rev. Sci. Instrum. 1998, 69:4094-4105.
46. Guevremont R., Purves R.W. Atmospheric Pressure Ion Focusing in a High-Field Asymmetric Waveform Ion Mobility Spectrometer. Rev. Sci. Instrum. 1999, 70:1370-1383.
47. Guevremont R. High-Field Asymmetric Waveform Ion Mobility Spectrometry: A New Tool for Mass Spectrometry. J. Chromatogr. A 2004, 1058:3-19.
48. Sacristan E., Solis A.A. A Swept-Field Aspiration Condenser as an Ion-Mobility Spectrometer. IEEE Trans. Instrum. Measurement 1998, 47:769-775.
49. Solis A.A., Sacristan E. Designing the Measurement Cell of a Swept-Field Differential Aspiration Condenser. Revista Mexicana de Fisica 2006, 52:322-328.
50. Dwivedi P., Wu C., Matz L.M., Clowers B.H., Siems W.F., Hill H.H. Gas-Phase Chiral Separations by Ion Mobility Spectrometry. Anal. Chem. 2006, 78:8200-8206.
51. Giles K., Pringle S.D., Worthington K.R., Little D., Wildgoose J.L., Bateman R.H. Applications of a Traveling Wave-Based Radio-Frequency-Only Stacked Ring Ion Guide. Rapid Commun. Mass Spectrom. 2004, 18:2401-2414.
52. Pringle S.D., Giles K., Wildgoose J.L., Williams J.P., Slade S.E., Thalassinos K., Bateman R.H., Bowers M.T., Scrivens J.H. An Investigation of the Mobility Separation of Some Peptide and Protein Ions Using a New Hybrid Quadrupole/Traveling Wave IMS/oa-TOF instrument. Int. J. Mass Spectrom. 2007, 261:1-12.
53. Williams J.P., Bugarcic T., Habtemariam A., Giles K., Campuzano I., Rodger P.M., Sadler P.J. Isomer Separation and Gas-Phase Configurations of Organoruthenium Anticancer Complexes: Ion Mobility Mass Spectrometry and Modeling. J. Am. Soc. Mass Spectrom. 2009, 6:1119-1122.
54. Hilton G.R., Thalassinos K., Grabenauer M., Sanghera N., Slade S.E., Wyttenbach T., Robinson P.J., Pinheiro T.J.T., Bowers M.T., Scrivens J.H. Structural Analysis of Prion Proteins by Means of Drift Cell and Traveling Wave Ion Mobility Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2010, 21:845-854.
55. Scarff C., Patel V.J., Thalassinos K., Scrivens J.H. Probing Hemoglobin Structure by Means of Traveling-Wave Ion Mobility Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2009, 20:625-631.
56. Smith D.P., Giles K., Bateman R.H., Radford S.E., Ashcroft A.E. Monitoring Co-Populated Conformational States During Protein Folding Events Using Electrospray Ionization-Ion Mobility Spectrometry-Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2007, 18:2180-2190.
57. Van Duijn E., Barendregt A., Synowsky S., Versluis C., Heck A.J.R. Chaperonin Complexes Monitored by Ion Mobility Mass Spectrometry. J. Am. Chem. Soc. 2009, 131:1452-1459.
58. Pukala T.L., Ruotolo B.T., Zhou M., Politis A., Stefanescu A., Leary J.A., Robinson C.V. Subunit Architecture of Multiprotein Assemblies Determined Using Restraints from Gas-Phase Measurements. Structure 2009, 17:1235-1243.
59. Hyung S.-J., Robinson C.V., Ruotolo B.T. Gas-Phase Unfolding and Disassembly Reveals Stability Differences in Ligand-Bound Multiprotein Complexes. Chem. Biol. 2009, 16:382-390.
60. Ruotolo B.T., Benesch J.L.P., Sandercock A.M., Hyung S.-J., Robinson C.V. Ion Mobility-Mass Spectrometry Analysis of Large Protein Complexes. Nature Prot. 2008, 3:1139-1152.
61. Hill H.H., Hill C.H., Asbury G.R., Wu C., Matz L.M., Ichiye T. Charge Location on Gas-Phase Peptides. Int. J. Mass Spectrom. 2002, 219:23-37.
62. Ruotolo B.T., Gillig K.J., Woods A.S., Egan T.F., Ugarov M.V., Schultz J.; A., Russel D.H. Analysis of Phosphorylated Peptides by Ion Mobility-Mass Spectrometry. Anal. Chem. 2004, 76:6727-6733.
63. Thalassinos K., Grabenauer M., Slade S.E., Hilton G.R., Bowers M.T., Scrivens J. H.; Characterization of Phosphorylated Peptides Using Traveling Wave-Based and Drift Cell Ion Mobility Mass Spectrometry. Anal. Chem. 2009, 81:248-254.
64. Zaia J., Campuzano I., Giles K., Bateman R., Keith C., Costello C.E. Electrospray Ion Mobility Spectrometry of Isomeric Carbohydrates. Glycobiology 2006, 11. 1140-1140.
65. Benassi M., Corilo Y.E., Uria D., Augusti R., Eberlin M.N. Recognition and Resolution of Isomeric Alkyl Anilines by Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2009, 20:269-277.
66. Campuzano, I.; Giles, K. SYNAPT G2 High Definition Mass Spectrometry: Ion Mobility Separation and Structural Elucidation of Natural Product Structural Isomers (2009). Retrieved August 13, 2010 from the website: http://www.waters.com/webassets/cms/library/docs/720003041en.pdf.
67. Campuzano, I.; Giles, K.; Neeson, K.; Richardson, K. SYNAPT G2 High Definition Mass Spectrometry: Separation and Collision Cross-Section Determination of Leucine and Isoleucine by Traveling Wave Ion Mobility Mass Spectrometry (2009). Retrieved August 13, 2010 from the website: http://www.waters.com/webassets/cms/library/docs/720003028en.pdf.
68. Riba-Garcia I., Giles K., Bateman R.H., Gaskell S.J. Evidence for Structural Variants of a- and b-Type Peptide Fragment Ions Using Combined Ion Mobility/Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2008, 19:608-613.
69. Guo X., Bandyopadhyay P., Schilling B., Young M.M., Fujii N., Aynechi T., Guy R.K., Kuntz I.D., Gibson B.W. Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking. Anal. Chem. 2008, 80:951-960.
70. Mädler S., Bich C., Touboul D., Zenobi R. Chemical Cross-Linking with NHS Esters: A Systematic Study on Amino Acid Reactivities. J. Mass Spectrom. 2009, 44:694-706.