Characterization of an ion mobility-multiplexed collision-induced dissociation-tandem time-of-flight mass spectrometry approach

International Journal of Mass Spectrometry

Volumn 293, Issue 1-3, 2010, Pages 34-44

  Ibrahim, Yehia M ^a   Prior, David C ^a   Baker, Erin S ^a   Smith, Richard D ^a   Belov, Mikhail E ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

False discovery rate; Ion mobility spectrometry; Multiplexed CID; Peptide identification; Time of flight

Indexed keywords

EID: 77955049296     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2010.03.009     Document Type: Article

References (48)

1. Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature 2003, 422(6928):198-207.
2. Wells J.M., McLuckey S.A. Biol. Mass Spectrom. 2005, vol. 402. Elsevier Academic Press Inc., San Diego, pp. 148-185.
3. Zubarev R.A., Kelleher N.L., McLafferty F.W. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 1998, 120(13):3265-3266.
4. Zubarev R.A., Horn D.M., Fridriksson E.K., Kelleher N.L., Kruger N.A., Lewis M.A., Carpenter B.K., McLafferty F.W. Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem. 2000, 72(3):563-573.
5. 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. 2004, 101(26):9528-9533.
6. Coon J.J., Syka J.E.P., Shabanowitz J., Hunt D.F. Tandem mass spectrometry for peptide and protein sequence analysis. BioTechniques 2005, 38(4):519-523.
7. Smith R.D. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2002, 2(5):513-523.
8. Masselon C., Anderson G.A., Harkewicz R., Bruce J.E., Paša-Tolić L., Smith R.D. Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. Anal. Chem. 2000, 72(8):1918-1924.
9. Masselon C., Paša-Tolić L., Lee S.-W., Li L., Anderson G.A., Harkewicz R., Smith R.D. Identification of tryptic peptides from large databases using multiplexed tandem mass spectrometry: simulations and experimental results. Proteomics 2003, 3(7):1279-1286.
10. Li L., Masselon C.D., Anderson G.A., Paša-Tolić L., Lee S.-W., Shen Y., Zhao R., Lipton M.S., Conrads T.P., Tolic N., Smith R.D. High-throughput peptide identification from protein digests using data-dependent multiplexed tandem FTICR mass spectrometry coupled with capillary liquid chromatography. Anal. Chem. 2001, 73(14):3312-3322.
11. Purvine S., Eppel J.T., Yi E.C., Goodlett D.R. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 2003, 3:847-850.
12. Chakraborty A.B., Berger S.J., John C. Gebler use of an integrated MS-multiplexed MS/MS data acquisition strategy for high-coverage peptide mapping studies. Rapid Commun. Mass Spectrom. 2007, 21(5):730-744.
13. Geromanos S.J., Vissers J.P.C., Silva J.C., Dorschel C.A., Li G.Z., Gorenstein M.V., Bateman R.H., Langridge J.I. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 2009, 9(6):1683-1695.
14. Wilson J., Vachet R.W. Multiplexed MS/MS in a quadrupole ion trap mass spectrometer. Anal. Chem. 2004, 76(24):7346-7353.
15. Lee Y.J., Hoaglund-Hyzer C.S., Taraszka J.A., Zientara G.A., Counterman A.E., Clemmer D.E. Collision-induced dissociation of mobility-separated ions using an orifice-skimmer cone at the back of a drift tube. Anal. Chem. 2001, 73(15):3549-3555.
16. Hoaglund-Hyzer C.S., Lee Y.J., Counterman A.E., Clemmer D.E. Coupling ion mobility separations, collisional activation techniques, and multiple stages of MS for analysis of complex peptide mixtures. Anal. Chem. 2002, 74(5):992-1006.
17. Baker E.S., Tang K., Danielson W.F., Prior D.C., Smith R.D. Simultaneous fragmentation of multiple ions using IMS drift time dependent collision energies. J. Am. Soc. Mass Spectrom. 2008, 19(3):411-419.
18. Becker C., Fernandez-Lima F.A., Gillig K.J., Russell W.K., Cologna S.M., Russell D.H. A novel approach to collision-induced dissociation (CID) for ion mobility-mass spectrometry experiments. J. Am. Soc. Mass Spectrom. 2009, 20(6):907-914.
19. Valentine S.J., Koeniger S.L., Clemmer D.E. A split-field drift tube for separation and efficient fragmentation of biomolecular ions. Anal. Chem. 2003, 75(22):6202-6208.
20. Purvine S., Eppel J.T., Yi E.C., Goodlett D.R. Proteomics 2003, 3(6):847-850.
21. Li G.Z., Vissers J.P.C., Silva J.C., Golick D., Gorenstein M.V., Geromanos S.J. Structural analysis of synthetic polymer mixtures using ion mobility and tandem mass spectrometry. Proteomics 2009, 9(6):1696-1719.
22. McDaniel E.W., Mason E.A. The Mobility and Diffusion of Ions in Gases 1973, John Wiley & Sons, New York.
23. Hoaglund-Hyzer C.S., Li J., Clemmer D.E. Mobility labeling for parallel CID of ion mixtures. Anal. Chem. 2000, 72(13):2737-2740.
24. Koeniger S.L., Valentine S.J., Myung S., Plasencia M., Lee Y.J., Clemmer D.E. Development of field modulation in a split-field drift tube for high-throughput multidimensional separations. J. Proteome Res. 2005, 4(1):25-35.
25. Lee J.L., Hoaglund-Hyzer C.S., Taraszka J.A., Zientara G.A., Counterman A.E., Clemmer D.E. Collision-induced dissociation of mobility-separated ions using an orifice-skimmer cone at the back of a drift tube. Anal. Chem. 2001, 73(15.).
26. 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. 2007, 261(1):1-12.
27. Giles K., Pringle S.D., Worthington K.R., Little D., Wildgoose J.L., Bateman R.H. Applications of a travelling wave-based radio-frequencyonly stacked ring ion guide. Rapid Commun. Mass Spectrom. 2004, 18(20):2401-2414.
28. Vakhrushev S.Y., Langridge J., Campuzano I., Hughes C., Peter-Katalinic J. Ion mobility mass spectrometry analysis of human glycourinome. Anal. Chem. 2008, 80(7):2506-2513.
29. 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(1):248-254.
30. Ibrahim Y.M., Belov M.E., Tolmachev A.V., Prior D.C., Smith R.D. Ion funnel trap interface for orthogonal time-of-flight mass spectrometry. Anal. Chem. 2007, 79(20):7845-7852.
31. Clowers B.H., Ibrahim Y.M., Prior D.C., Danielson W.F., Belov M.E., Smith R.D. Enhanced ion utilization efficiency using an electrodynamic ion funnel trap as an injection mechanism for ion mobility spectrometry. Anal. Chem. 2008, 80(3):612-623.
32. Shaffer S.A., Tang K., Anderson G.A., Prior D.C., Udseth H.R., Smith R.D. A novel ion funnel for focusing ions at elevated pressure using electrospray ionization mass spectrometry. Rapid Commun. Mass Spectrom. 1997, 11:1813-1817.
33. Belov M.E., Gorshkov M.V., Udseth H.R., Anderson G.A., Tolmachev A.V., Prior D.C., Harkewicz R., Smith R.D. Initial implementation of an electrodynamic ion funnel with Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 2000, 11(1):19-23.
34. Kinter M.M., Sherman N.E. Protein Sequencing and Identification Using Tandem Mass Spectrometry 2000, Wiley-Interscience, New York.
35. Jaitly N., Mayampurath A., Littlefield K., Adkins J., Anderson G., Smith R. Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinf. 2009, 10(1):87.
36. Decon2ls, http://omics.pnl.gov/software/.
37. Horn D.M., Zubarev R.A., McLafferty F.W. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 2000, 11(4):320-332.
38. Protein Digestion Simulator, http://omics.pnl.gov/software/.
39. Yost R.A., Enke C.G., McGilvery D.C., Smith D., Morrison J.D. High efficiency collision-induced dissociation in an RF-only quadrupole. Int. J. Mass Spectrom. Ion Phys. 1979, 30(2):127-136.
40. Thomson B.A., Douglas D.J., Corr J.J., Hager J.W., Jolliffe C.L. Improved collisionally activated dissociation efficiency and mass resolution on a triple quadrupole mass spectrometer system. Anal. Chem. 1995, 67(10):1696-1704.
41. Belov M.E., Clowers B.H., Prior D.C., Danielson Iii W.F., Liyu A.V., Petritis B.O., Smith R.D. Dynamically multiplexed ion mobility time-of-flight mass spectrometry. Anal. Chem. 2008, 80(15):5873-5883.
42. Cong Y.Z., Zhang L.H., Tao D.Y., Liang Y., Zhang W.B., Zhang Y.K. Miniaturized two-dimensional capillary electrophoresis on a microchip for analysis of the tryptic digest of proteins. J. Sep. Sci. 2008, 31(3):588-594.
43. Creese A.J., Cooper H.J. Liquid chromatography electron capture dissociation tandem mass spectrometry (LC-ECD-MS/MS) versus liquid chromatography collision-induced dissociation tandem mass spectrometry (LC-CID-MS/MS) for the identification of proteins. J. Am. Soc. Mass Spectrom. 2007, 18(5):891-897.
44. Francois I., Cabooter D., Sandra K., Lynen F., Desmet G., Sandra P. Tryptic digest analysis by comprehensive reversed phase x two reversed phase liquid chromatography (RP-LC x 2RP-LC) at different pH's. J. Sep. Sci. 2009, 32(8):1137-1144.
45. Kaur-Atwal G., Weston D.J., Green P.S., Crosland S., Bonner P.L.R., Creaser C.S. Analysis of tryptic peptides using desorption electrospray ionisation combined with ion mobility spectrometry/mass spectrometry. Rapid Commun. Mass Spectrom. 2007, 21(7):1131-1138.
46. Satoh T., Sato T., Tamura J. Development of a high-performance MALDI-TOF mass spectrometer utilizing a spiral ion trajectory. J. Am. Soc. Mass Spectrom. 2007, 18(7):1318-1323.
47. Ibrahim Y.M., Belov M.E., Liyu A.V., Smith R.D. Automated gain control ion funnel trap for orthogonal time-of-flight mass spectrometry. Anal. Chem. 2008, 80(14):5367-5376.
48. Belov M.E., Buschbach M.A., Prior D.C., Tang K., Smith R.D. Multiplexed ion mobility spectrometry-orthogonal time-of-flight mass spectrometry. Anal. Chem. 2007, 79(6):2451-2462.