Charge state coalescence during electrospray ionization improves peptide identification by tandem mass spectrometry

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 8, 2012, Pages 1390-1399

  Meyer, Jesse G ^a   Komives, Elizabeth A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DMSO; Elastase; Electron transfer dissociation; Electrospray ionization; M NBA; Non tryptic peptides; Pepsin; Peptide identification; Proteomics; Tandem mass spectrometry

Indexed keywords

DMSO; ELASTASE; ELECTRON TRANSFER DISSOCIATION; M-NBA; PEPSIN; PEPTIDE IDENTIFICATION; PROTEOMICS; TANDEM MASS SPECTROMETRY;

BIOLOGICAL MATERIALS; COALESCENCE; DISSOCIATION; ELECTROSPRAY IONIZATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; SOLVENTS;

PEPTIDES;

3 NITROBENZYL ALCOHOL; ALCOHOL DERIVATIVE; DIMETHYL SULFOXIDE; ELASTASE; FORMIC ACID; PEPSIN A; TRYPSIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; DISSOCIATION; ELECTRON TRANSFER DISSOCIATION; ELECTROSPRAY MASS SPECTROMETRY; HYDROGEN BOND; LIQUID CHROMATOGRAPHY; PEPTIDE ANALYSIS; PHASE SEPARATION; SEPARATION TECHNIQUE; SOLVENT EFFECT; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; BENZYL ALCOHOLS; DIMETHYL SULFOXIDE; MOLECULAR SEQUENCE DATA; PANCREATIC ELASTASE; PEPSIN A; PEPTIDE FRAGMENTS; PROTEINS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY; TRYPSIN;

EID: 84865770129     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0404-0     Document Type: Article

References (39)

1. Sleno, L., Volmer, D.A.: Ion activation methods for tandem mass spectrometry. J. Mass Spectrom. 39, 1091-1112 (2004) (Pubitemid 39409895)
2. Ong, S.-E., Mann, M.: Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262 (2005)
3. Motoyama III, A.J.R.Y.: Multidimensional LC separations in shotgun proteomics. Anal. Chem. 80, 7187-7193 (2008)
4. Fenn, J., Mann, M., Meng, C., Wong, S., Whitehouse, C.: Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71 (1989) (Pubitemid 19252085)
5. de Godoy, L.M.F., Olsen, J.V., Cox, J., Nielsen, M.L., Hubner, N.C., Frohlich, F., Walther, T.C., Mann, M.: Comprehensive mass-spectrometry- based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254 (2008)
6. Burkhart, J. M., Schumbrutzki, C., Wortelkamp, S., Sickmann, A., Zahedi, R. P.: Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MSbased proteomics. J. Proteom. 75, 1454-1462 (2012)
7. Tabb, D.L., Smith, L.L., Breci, L.A., Wysocki, V.H., Lin, D., Yates, J.R.: Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal. Chem. 75, 1155-1163 (2003) (Pubitemid 36402645)
8. Swaney, D.L., Wenger, C.D., Coon, J.J.: Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteom. Res. 9, 1323-1329 (2010)
9. Syka, J.E.P., Coon, J.J., Schroeder, M.J., Shabanowitz, J., Hunt, D.F.: Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101, 9528-9533 (2004) (Pubitemid 38869270)
10. Swaney, D.L., McAlister, G.C., Wirtala, M., Schwartz, J.C., Syka, J.E.P., Coon, J.J.: Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal. Chem. 79, 477-485 (2006) (Pubitemid 46110632)
11. Loo, J.A., Udseth, H.R., Smith, R.D., Futrell, J.H.: Collisional effects on the charge distribution of ions from large molecules, formed by electrospray-ionization mass spectrometry. Rapid Commun. Mass Spectrom. 2, 207-210 (1988)
12. Kamel, A.M., Brown, P.R., Munson, B.: Effects of mobile-phase additives, solution pH, ionization constant, and analyte concentration on the sensitivities and electrospray ionization mass spectra of nucleoside antiviral agents. Anal. Chem. 71, 5481-5492 (1999)
13. Mallet, C.R., Lu, Z., Mazzeo, J.R.: A study of ion suppression effects in electrospray ionization from mobile phase additives and solid-phase extracts. Rapid Commun. Mass Spectrom. 18, 49-58 (2004) (Pubitemid 38031417)
14. Ficarro, S.B., Zhang, Y., Lu, Y., Moghimi, A.R., Askenazi, M., Hyatt, E., Smith, E.D., Boyer, L., Schlaeger, T.M., Luckey, C.J., Marto, J.A.: Improved electrospray ionization efficiency compensates for diminished chromatographic resolution and enables proteomics analysis of tyrosine signaling in embryonic stem cells. Anal. Chem. 81, 3440-3447 (2009)
15. Rayleigh, L.: On the equilibrium of liquid conducting masses charged with electricity. Phils. Mag. 14, 184-186 (1882)
16. Iavarone, A.T., Williams, E.R.: Supercharging in electrospray ionization: Effects on signal and charge. Int. J. Mass Spectrom. 219, 63-72 (2002)
17. Iavarone, A.T., Williams, E.R.: Mechanism of charging and supercharging molecules in electrospray ionization. J. Am. Chem. Soc. 125, 2319-2327 (2003) (Pubitemid 36245725)
18. Kjeldsen, F., Giessing, A.M., Ingrell, C.R., Jensen, O.N.: Peptide sequencing and characterization of post-translational modifications by enhanced ion-charging and liquid chromatography electron-transfer dissociation tandem mass spectrometry. Anal. Chem. 79, 9243-9252 (2007) (Pubitemid 350276301)
19. Sterling, H.J., Williams, E.R.: Real-time hydrogen/deuterium exchange kinetics via supercharged electrospray ionization tandem mass spectrometry. Anal. Chem. 82, 9050-9057 (2010)
20. Yin, S., Loo, J.A.: Top-down mass spectrometry of supercharged native protein-ligand complexes. Int. J. Mass Spectrom. 300, 118-122 (2011)
21. Valeja, S.G., Tipton, J.D., Emmett, M.R., Marshall, A.G.: New reagents for enhanced liquid chromatographic separation and charging of intact protein ions for electrospray ionization mass spectrometry. Anal. Chem. 82, 7515-7519 (2010)
22. Lomeli, S.H., Peng, I.X., Yin, S., Ogorzalek Loo, R.R., Loo, J.A.: New reagents for increasing ESI multiple charging of proteins and protein complexes. J. Am. Soc. Mass Spectrom. 21, 127-131 (2010)
23. Douglass, K.A., Venter, A.R.: Investigating the role of adducts in protein supercharging with sulfolane. J. Am. Soc. Mass Spectrom. 23, 489-497 (2012)
24. Hogan, J.C.J., Biswas, P.: Monte Carlo simulation of macromolecular ionization by nanoelectrospray. J. Am. Soc. Mass Spectrom. 19, 1098- 1107 (2008)
25. Wilm, M.: Principles of electrospray ionization. Mol. Cell. Proteomics 10, 1-8 (2011)
26. Ahadi, E., Konermann, L.: Modeling the behavior of coarse-grained polymer chains in charged water droplets: Implications for the mechanism of electrospray ionization. J. Phys. Chem. B (2011)
27. Sterling, H.J., Daly, M.P., Feld, G.K., Thoren, K.L., Kintzer, A.F., Krantz, B.A., Williams, E.R.: Effects of supercharging reagents on noncovalent complex structure in electrospray ionization from aqueous solutions. J. Am. Soc. Mass Spectrom. 21, 1762-1774 (2010)
28. Ogorzalek Loo, R.R., Smith, R.D.: Proton transfer reactions of multiply charged peptide and protein cations and anions. J. Mass Spectrom. 30, 339-347 (1995)
29. Coulier, L., Bas, R., Jespersen, S., Verheij, E., van der Werf, M.J., Hankemeier, T.: Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatography-electrospray ionization mass spectrometry. Anal. Chem. 78, 6573-6582 (2006) (Pubitemid 44413611)
30. Gustavsson, S.Å., Samskog, J., Markides, K.E., Långströ m, B.: Studies of signal suppression in liquid chromatography-electrospray ionization mass spectrometry using volatile ion-pairing reagents. J. Chromatogr. A 937, 41-47 (2001) (Pubitemid 33079154)
31. Swaney, D.L., McAlister, G.C., Coon, J.J.: Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Methods 5, 959-964 (2008)
32. Kim, M.-S., Zhong, J., Kandasamy, K., Delanghe, B., Pandey, A.: Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics 11, 2568-2572 (2011)
33. Kim, S., Mischerikow, N., Bandeira, N., Navarro, J.D., Wich, L., Mohammed, S., Heck, A.J.R., Pevzner, P.A.: The generating function of CID, ETD and CID/ETD pairs of tandem mass spectra: Applications to database search. Mol. Cell. Proteomics 9, 2840-2852 (2010)
34. Lin, Y., Zhou, J., Bi, D., Chen, P., Wang, X., Liang, S.: Sodiumdeoxycholate- Assisted tryptic digestion and identification of proteolytically resistant proteins. Anal. Biochem. 377, 259-266 (2008)
35. Keller, A., Eng, J., Zhang, N., Li, X.-j., Aebersold, R.: A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1(2005)
36. Smith, C.A., Want, E.J., Tong, G.C., Abagyan, R., Siuzdak, G.: XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78, 779-787 (2006) (Pubitemid 43228585)
37. Development Core Team: A language and environment for statistical computing. Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/ (2012)
38. Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P.: ProteoWizard: Open source software for rapid proteomics tools development. Bioinformatics 24, 2534-2536 (2008)
39. Sterling, H.J., Prell, J.S., Cassou, C.A., Williams, E.R.: Protein conformation and supercharging with DMSO from aqueous solution. J. Am. Soc. Mass Spectrom. 22, 1178-1186 (2011)