Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies

Journal of Proteome Research

Volumn 12, Issue 6, 2013, Pages 2323-2339

  Shliaha, Pavel V ^a   Bond, Nicholas J ^a,b   Gatto, Laurent ^a   Lilley, Kathryn S ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b MRC HUMAN NUTRITION RESEARCH   (United Kingdom)

Author keywords

ion mobility separation; mass spectrometry; saturation; traveling wave ion mobility separation

Indexed keywords

PROTEOME;

ARTICLE; ATTENUATION; INFORMATION PROCESSING; MEASUREMENT; PRECURSOR; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; TRAVELING WAVE ION MOBILITY SEPARATION;

EID: 84879367507     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300775k     Document Type: Article

References (42)

1. Schulze, W. X.; Usadel, B. Quantitation in mass-spectrometry-based proteomics Annu. Rev. Plant Biol. 2010, 61, 491-516
2. Sadygov, R. G.; Cociorva, D.; Yates, J. R., 3rd Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book Nat. Methods 2004, 1, 195-202
3. Ong, S.-E.; Kratchmarova, I.; Mann, M. Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC) J. Proteome Res. 2003, 2, 173-181
4. Thompson, A.; Schäfer, J.; Kuhn, K.; Kienle, S.; Schwarz, J.; Schmidt, G.; Neumann, T.; Johnstone, R.; Mohammed, A. K. A.; Hamon, C. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS Anal. Chem. 2003, 75, 1895-1904
5. Neilson, K. A.; Ali, N. A.; Muralidharan, S.; Mirzaei, M.; Mariani, M.; Assadourian, G.; Lee, A.; van Sluyter, S. C.; Haynes, P. A. Less label, more free: approaches in label-free quantitative mass spectrometry Proteomics 2011, 11, 535-553
6. Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein Mol. Cell. Proteomics 2005, 4, 1265-1272
7. 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, 1683-1695
8. Gillet, L. C.; Navarro, P.; Tate, S.; Roest, H.; Selevsek, N.; Reiter, L.; Bonner, R.; Aebersold, R. Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis Mol. Cell. Proteomics 2012, 11 (6 O111.016717
9. Levin, Y.; Hradetzky, E.; Bahn, S. Quantification of proteins using data-independent analysis (MSE) in simple andcomplex samples: a systematic evaluation Proteomics 2011, 11, 3273-3287
10. Silva, J. C.; Denny, R.; Dorschel, C. A.; Gorenstein, M.; Kass, I. J.; Li, G.-Z.; McKenna, T.; Nold, M. J.; Richardson, K.; Young, P.; Geromanos, S. Quantitative proteomic analysis by accurate mass retention time pairs Anal. Chem. 2005, 77, 2187-2200
11. Silva, J. C.; Gorenstein, M. V.; Li, G.-Z.; Vissers, J. P. C.; Geromanos, S. J. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition Mol. Cell. Proteomics 2006, 5, 144-156
12. Li, G.-Z.; Vissers, J. P. C.; Silva, J. C.; Golick, D.; Gorenstein, M. V.; Geromanos, S. J. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures Proteomics 2009, 9, 1696-1719
13. Valentine, S. J.; Ewing, M. A.; Dilger, J. M.; Glover, M. S.; Geromanos, S.; Hughes, C.; Clemmer, D. E. Using Ion Mobility Data to Improve Peptide Identification: Intrinsic Amino Acid Size Parameters J. Proteome Res. 2011, 10, 2318-2329
14. Shah, A. R.; Agarwal, K.; Baker, E. S.; Singhal, M.; Mayampurath, A. M.; Ibrahim, Y. M.; Kangas, L. J.; Monroe, M. E.; Zhao, R.; Belov, M. E.; Anderson, G. A.; Smith, R. D. Machine learning based prediction for peptide drift times in ion mobility spectrometry Bioinformatics 2010, 26, 1601-1607
15. Chamrad, D.; Meyer, H. E. Valid data from large-scale proteomics studies Nat. Methods 2005, 2, 647-648
16. Miyamoto, M.; Yoshida, Y.; Taguchi, I.; Nagasaka, Y.; Tasaki, M.; Zhang, Y.; Xu, B.; Nameta, M.; Sezaki, H.; Cuellar, L. M.; Osawa, T.; Morishita, H.; Sekiyama, S.; Yaoita, E.; Kimura, K.; Yamamoto, T. In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry J. Proteome Res. 2007, 6, 3680-3690
17. Michalski, A.; Cox, J.; Mann, M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS J. Proteome Res. 2011, 10, 1785-1793
18. Kennedy, J.; Yi, E. C. Use of gas-phase fractionation to increase protein identifications: application to the peroxisome Methods Mol. Biol. 2008, 432, 217-228
19. Masselon, C.; Anderson, G. A.; Harkewicz, R.; Bruce, J. E.; Pasa-Tolic, L.; Smith, R. D. Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures Anal. Chem. 2000, 72, 1918-1924
20. Panchaud, A.; Scherl, A.; Shaffer, S. A.; von Haller, P. D.; Kulasekara, H. D.; Miller, S. I.; Goodlett, D. R. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean Anal. Chem. 2009, 81, 6481-6488
21. Venable, J. D.; Dong, M.-Q.; Wohlschlegel, J.; Dillin, A.; Yates, J. R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra Nat. Methods 2004, 1, 39-45
22. Geiger, T.; Cox, J.; Mann, M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation Mol. Cell. Proteomics 2010, 9, 2252-2261
23. Myung, S.; Lee, Y. J.; Moon, M. H.; Taraszka, J.; Sowell, R.; Koeniger, S.; Hilderbrand, A. E.; Valentine, S. J.; Cherbas, L.; Cherbas, P.; Kaufmann, T. C.; Miller, D. F.; Mechref, Y.; Novotny, M. V.; Ewing, M. A.; Sporleder, C. R.; Clemmer, D. E. Development of high-sensitivity ion trap ion mobility spectrometry time-of-flight techniques: a high-throughput nano-LC-IMS-TOF separation of peptides arising from a Drosophila protein extract Anal. Chem. 2003, 75, 5137-5145
24. Valentine, S. J.; Plasencia, M. D.; Liu, X.; Krishnan, M.; Naylor, S.; Udseth, H. R.; Smith, R. D.; Clemmer, D. E. Toward Plasma Proteome Profiling with Ion Mobility-Mass Spectrometry J. Proteome Res. 2006, 5, 2977-2984
25. Taraszka, J. A.; Kurulugama, R.; Sowell, R. A.; Valentine, S. J.; Koeniger, S. L.; Arnold, R. J.; Miller, D. F.; Kaufman, T. C.; Clemmer, D. E. Mapping the proteome of Drosophila melanogaster: analysis of embryos and adult heads by LC-IMS-MS methods J. Proteome Res. 2005, 4, 1223-1237
26. Hoaglund-Hyzer, C. S.; Li, J.; Clemmer, D. E. Mobility labeling for parallel CID of ion mixtures Anal. Chem. 2000, 72, 2737-2740
27. Baker, E. S.; Livesay, E. A.; Orton, D. J.; Moore, R. J.; Danielson, W. F., 3rd; Prior, D. C.; Ibrahim, Y. M.; LaMarche, B. L.; Mayampurath, A. M.; Schepmoes, A. A.; Hopkins, D. F.; Tang, K.; Smith, R. D.; Belov, M. E. An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies J. Proteome Res. 2010, 9, 997-1006
28. Geromanos, S. J.; Hughes, C.; Ciavarini, S.; Vissers, J. P. C.; Langridge, J. I. Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples Anal. Bioanal. Chem. 2012, 404 (4) 1127-1139
29. Valentine, S. J.; Counterman, A. E.; Hoaglund, C. S.; Reilly, J. P.; Clemmer, D. E. Gas-phase separations of protease digests J. Am. Soc. Mass Spectrom. 1998, 9, 1213-1216
30. Bohrer, B. C.; Merenbloom, S. I.; Koeniger, S. L.; Hilderbrand, A. E.; Clemmer, D. E. Biomolecule analysis by ion mobility spectrometry Annu. Rev. Anal. Chem. 2008, 1, 293-327
31. Hoaglund, C. S.; Valentine, S. J.; Clemmer, D. E. An Ion Trap Interface for ESI-Ion Mobility Experiments Anal. Chem. 1997, 69, 4156-4161
32. Davis, E. J.; Grows, K. F.; Siems, W. F.; Hill, H. H., Jr Improved ion mobility resolving power with increased buffer gas pressure Anal. Chem. 2012, 84, 4858-4865
33. Moore, S.; Spackman, D. H.; Stein, W. H. Automatic recording apparatus for use in the chromatography of amino acids Fed. Proc. 1958, 17, 1107-1115
34. Geromanos, S. J.; Hughes, C.; Golick, D.; Ciavarini, S.; Gorenstein, M. V.; Richardson, K.; Hoyes, J. B.; Vissers, J. P. C.; Langridge, J. I. Simulating and validating proteomics data and search results Proteomics 2011, 11, 1189-1211
35. Davis, E. J.; Dwivedi, P.; Tam, M.; Siems, W. F.; Hill, H. H. High-pressure ion mobility spectrometry Anal. Chem. 2009, 81, 3270-3275
36. Tang, K.; Shvartsburg, A. A.; Lee, H.-N.; Prior, D. C.; Buschbach, M. A.; Li, F.; Tolmachev, A.; Anderson, G. A.; Smith, R. D. High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic Ion Funnel Interfaces Anal. Chem. 2005, 77, 3330-3339
37. 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, 3549-3555
38. 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
39. Kelly, R. T.; Tolmachev, A. V.; Page, J. S.; Tang, K.; Smith, R. D. The ion funnel: theory, implementations, and applications Mass Spectrom. Rev. 2010, 29, 294-312
40. Chernushevich, I. V.; Loboda, A. V.; Thomson, B. A. An introduction to quadrupole-time-of-flight mass spectrometry J. Mass Spectrom. 2001, 36, 849-865
41. Ghaemmaghami, S.; Huh, W.-K.; Bower, K.; Howson, R. W.; Belle, A.; Dephoure, N.; O'Shea, E. K.; Weissman, J. S. Global analysis of protein expression in yeast Nature 2003, 425, 737-741
42. E-based label-free proteomics J. Proteome Res. 2013, 10.1021/pr300776k