Combined use of post-ion mobility/collision-induced dissociation and chemometrics for b fragment ion analysis

Journal of the American Society for Mass Spectrometry

Volumn 24, Issue 9, 2013, Pages 1355-1365

  Zekavat, Behrooz ^a   Miladi, Mahsan ^a   Becker, Christopher ^a   Munisamy, Sharon M ^a   Solouki, Touradj ^a  

^a BAYLOR UNIVERSITY   (United States)

Author keywords

b Fragment ions; Chemometrics; Collision induced dissociation (CID); Ion mobility spectrometry (IMS); Mass spectrometry (MS); Principle component analysis (PCA)

Indexed keywords

CHEMOMETRICS; COLLISION-INDUCED DISSOCIATION; FRAGMENT IONS; ION MOBILITY SPECTROMETRY; PRINCIPLE COMPONENT ANALYSIS;

DISSOCIATION; DRUG PRODUCTS; IONS; MASS SPECTROMETERS; MASS SPECTROMETRY; PRINCIPAL COMPONENT ANALYSIS;

ISOMERS;

B FRAGMENT ION; HEPTAPEPTIDE; ION; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; CHEMOMETRIC ANALYSIS; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; FRAGMENTATION REACTION; ION MOBILITY SPECTROMETRY; ISOMER; SIMPLE TO USE INTERACTIVE SELF MODELING MIXTURE ANALYSIS; STRUCTURE ANALYSIS; TANDEM MASS SPECTROMETRY;

EID: 84881577886     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-013-0673-2     Document Type: Article

References (43)

1. Chait, B.T.: Mass spectrometry: Bottom-up or top-down? Science 314, 65-66 (2006)
2. Baldwin, M.A.: Protein identification by mass spectrometry: Issues to be considered. Mol. Cell. Proteom. 3, 1-9 (2004)
3. Elias, J.E.; Gygi, S.P.: Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214 (2007)
4. Lam, H.; Aebersold, R.: Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics. Methods 54, 424-431 (2011)
5. Lubec, G.; Afjehi-Sadat, L.: Limitations and pitfalls in protein identification by mass spectrometry. Chem. Rev. 107, 3568-3584 (2007)
6. Harrison, A.G.; Young, A.B.; Bleiholder, C.; Suhai, S.; Paizs, B.: Scrambling of sequence information in collision-induced dissociation of peptides. J. Am. Chem. Soc. 128, 10364-10365 (2006)
7. Nesvizhskii, A.I.; Vitek, O.; Aebersold, R.: Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4, 787-797 (2007)
8. Roepstorff, P.; Fohlman, J.: Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11, 601 (1984)
9. Tang, X.J.; Boyd, R.K.: Rearrangements of doubly charged acylium ions from lysyl and ornithyl peptides. Rapid Commun. Mass Spectrom. 8, 678-686 (1994)
10. Fattahi, A.; Solouki, T.: Conformational analysis of metal complexed model peptides and their fragment ions using FT-ICR MS and gas-phase H/D exchange reactions. Proceedings of the 49th ASMS Conference on Mass Spectrometry and Allied Topics Chicago, IL (2001)
11. Somogyi, A.: Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments. J. Am. Soc. Mass Spectrom. 19, 1771-1775 (2008)
12. 8. J. Am. Chem. Soc. 131, 18272-18282 (2009)
13. + ion. J. Am. Chem. Soc. 131, 17528-17529 (2009)
14. 4: Insights from infrared multiple-photon dissociation spectroscopy and gas-phase hydrogen/deuterium exchange. J. Am. Soc. Mass Spectrom. 21, 1313-1321 (2010)
15. Fattahi, A.; Zekavat, B.; Solouki, T.: H/D exchange kinetics: Experimental evidence for formation of different b fragment ion conformers/isomers during the gas-phase peptide sequencing. J. Am. Soc. Mass Spectrom. 21, 358-369 (2010)
16. n ions. Int. J. Mass Spectrom 316/318, 164-173 (2012)
17. Paizs, B.; Suhai, S.: Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24, 508-548 (2005)
18. Bythell, B.J.; Knapp-Mohammady, M.; Paizs, B.; Harrison, A.G.: Effect of the His residue on the cyclization of b ions. J. Am. Soc. Mass Spectrom. 21, 1352-1363 (2010)
19. Polfer, N.C.; Bohrer, B.C.; Plasencia, M.D.; Paizs, B.; Clemmer, D.E.: On the dynamics of fragment isomerization in collision-induced dissociation of peptides. J. Phys. Chem. A 112, 1286-1293 (2008)
20. Riba Garcia, I.; Giles, K.; Bateman, R.H.; Gaskell, S.J.: Studies of peptide a- and b-type fragment ions using stable isotope labeling and integrated ion mobility/tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 19, 1781-1787 (2008)
21. Riba-Garcia, I.; Giles, K.; Bateman, R.H.; Gaskella, 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. 19, 609-613 (2008)
22. + ion. J. Am. Chem. Soc. 130, 17644-17645 (2008)
23. 5 ions. J. Am. Chem. Soc. 131, 11503-11508 (2009)
24. n fragment ions. Proceedings of the 58th ASMS Conference on Mass Spectrometry and Allied Topics. Salt Lake City, UT, May 23-27 (2010)
25. Lee, S.; Li, Z.; Valentine, S.J.; Zucker, S.M.; Webber, N.; Reilly, J.P.; Clemmer, D.E.: Extracted fragment ion mobility distributions: A new method for complex mixture analysis. Int. J. Mass Spectrom. 309, 154-160 (2012)
26. Creese, A.J.; Cooper, H.J.: Separation and identification of isomeric glycopeptides by high field asymmetric waveform ion mobility spectrometry. Anal. Chem. 84, 2597-2601 (2012)
27. Zekavat, B.; Solouki, T.: Chemometric data analysis for deconvolution of overlapped ion mobility profiles. J. Am. Soc. Mass Spectrom. 23, 1873-1884 (2012)
28. Bateman, R.H.; Carruthers, R.; Hoyes, J.B.; Jones, C.; Langridge, J.I.; Millar, A.; Vissers, J.P.C.: A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation. J. Am. Soc. Mass Spectrom. 13, 792-803 (2002)
29. 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/travelling wave IMS/oa-ToF instrument. Int. J. Mass Spectrom. 261, 1-12 (2007)
30. Pedrioli, P.G.; Eng, J.K.; Hubley, R.; Vogelzang, M.; Deutsch, E.W.; Raught, B.; Pratt, B.; Nilsson, E.; Angeletti, R.H.; Apweiler, R.; Cheung, K.; Costello, C.E.; Hermjakob, H.; Huang, S.; Julian, R.K.; Kapp, E.; McComb, M.E.; Oliver, S.G.; Omenn, G.; Paton, N.W.; Simpson, R.; Smith, R.; Taylor, C.F.; Zhu, W.; Aebersold, R.: A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22, 1459-1466 (2004)
31. massWolf4.3.1. Available at: http://sourceforge.net/projects/sashimi/ 2009. Last accessed: March 05, 2012
32. Meloun, M.; Čapek, J.; Mikšík, P.; Brereton, R.G.: Critical comparison of methods predicting the number of components in spectroscopic data. Anal. Chim. Acta 423, 51-68 (2000)
33. Windig, W.; Guilment, J.: Interactive self-modeling mixture analysis. Anal. Chem. 63, 1425-1432 (1991)
34. Ruotolo, B.T.; Benesch, J.L.; Sandercock, A.M.; Hyung, S.J.; Robinson, C.V.: Ion mobility-mass spectrometry analysis of large protein complexes. Nat. Protoc. 3, 1139-1152 (2008)
35. Malinowski, E.R.: Determination of the number of factors and the experimental error in a data matrix. Anal. Chem. 49, 612-617 (1977)
36. Szulejko, J.E.; Solouki, T.: Potential analytical applications of interfacing a GC to an FT-ICR MS: Fingerprinting complex sample matrixes. Anal. Chem. 74, 3434-3442 (2002)
37. Peng, J.; Elias, J.E.; Thoreen, C.C.; Licklider, L.J.; Gygi, S.P.: Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2, 43-50 (2003)
38. Bleiholder, C.; Osburn, S.; Williams, T.D.; Suhai, S.; Van Stipdonk, M.; Harrison, A.G.; Paizs, B.: Sequence-scrambling fragmentation pathways of protonated peptides. J. Am. Chem. Soc. 130, 17774-17789 (2008)
39. Molesworth, S.; Osburn, S.; Van Stipdonk, M.: Influence of size on apparent scrambling of sequence during CID of b-type ions. J. Am. Soc. Mass Spectrom. 20, 2174-2181 (2009)
40. Morsa, D.; Gabelica, V.; De Pauw, E.: Effective temperature of ions in traveling wave ion mobility spectrometry. Anal. Chem. 83, 5775-5782 (2011)
41. Merenbloom, S.I.; Flick, T.G.; Williams, E.R.: How hot are your ions in TWAVE ion mobility spectrometry? J. Am. Soc. Mass Spectrom. 23, 553-562 (2012)
42. Giles, K.; Williams, J.P.; Campuzano, I.: Enhancements in travelling wave ion mobility resolution. Rapid Commun. Mass Spectrom. 25, 1559-1566 (2011)
43. Sawyer, H.A.; Marini, J.T.; Stone, E.G.; Ruotolo, B.T.; Gillig, K.J.; Russell, D.H.: The structure of gas-phase bradykinin fragment 1-5 (RPPGF) ions: An ion mobility spectrometry and H/D exchange ion-molecule reaction chemistry study. J. Am. Soc. Mass Spectrom. 16, 893-905 (2005)