Distinguishing analyte from noise components in mass spectra of complex samples: Where to cut the noise?

Analytical Chemistry

Volumn 86, Issue 7, 2014, Pages 3308-3316

  Zhurov, Konstantin O ^a   Kozhinov, Anton N ^a   Fornelli, Luca ^a   Tsybin, Yury O ^a  

^a EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MASS SPECTROMETERS; MIXTURES;

COMPREHENSIVE ANALYSIS; CRUDE OIL FRACTIONS; FOURIER TRANSFORM MASS SPECTROMETRY; MOLECULAR MIXTURES; NOISE COMPONENTS; NOISE THRESHOLDS; SPECTRAL AMPLITUDE; THRESHOLDING METHODS;

MASS SPECTROMETRY;

FOURIER ANALYSIS; MASS SPECTROMETRY; PROCEDURES; SIGNAL NOISE RATIO;

FOURIER ANALYSIS; MASS SPECTROMETRY; SIGNAL-TO-NOISE RATIO;

EID: 84897549872     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac403278t     Document Type: Article

References (63)

1. Schaub, T. M.; Hendrickson, C. L.; Horning, S.; Quinn, J. P.; Senko, M. W.; Marshall, A. G. Anal. Chem. 2008, 80, 3985-3990
2. Michalski, A.; Damoc, E.; Lange, O.; Denisov, E.; Nolting, D.; Mueller, M.; Viner, R.; Schwartz, J.; Remes, P.; Belford, M.; Dunyach, J.-J.; Cox, J.; Horning, S.; Mann, M.; Makarov, A. Mol. Cell. Proteomics 2012, 11, 013698/1-013698/11
3. Savory, J. J.; Kaiser, N. K.; McKenna, A. M.; Xian, F.; Blakney, G. T.; Rodgers, R. P.; Hendrickson, C. L.; Marshall, A. G. Anal. Chem. 2011, 83, 1732-1736
4. Qi, Y.; Barrow, M. P.; Li, H.; Meier, J. E.; Van Orden, S. L.; Thompson, C. J.; O'Connor, P. B. Anal. Chem. 2012, 84, 2923-2929
5. Zhurov, K. O.; Kozhinov, A. N.; Tsybin, Y. O. Energy Fuels 2013, 27, 2974-2983
6. Belov, M. E.; Nikolaev, E. N.; Anderson, G. A.; Auberry, K. J.; Harkewicz, R.; Smith, R. D. J. Am. Soc. Mass Spectrom. 2001, 12, 38-48
7. Marshall, A. G.; Rodgers, R. P. Acc. Chem. Res. 2004, 37, 53-59
8. Ding, X.; Ghobarah, H.; Zhang, X.; Jaochico, A.; Liu, X.; Deshmukh, G.; Liederer, B. M.; Hop, C. E. C. A.; Dean, B. Rapid Commun. Mass Spectrom. 2013, 27, 401-408
9. Marshall, A. G.; Chen, T.; Xian, F.; Kaiser, N. K.; Quinn, J. P.; Beu, S. C.; Hendrickson, C. L. Proceedings of the 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, Canada, May 20-24, 2012.
10. Enke, C. G.; Nagels, L. J. Anal. Chem. 2011, 83, 2539-2546
11. Picotti, P.; Bodenmiller, B.; Mueller, L. N.; Domon, B.; Aebersold, R. Cell 2009, 138, 795-806
12. Castro-Marcano, F.; Lobodin, V. V.; Rodgers, R. P.; McKenna, A. M.; Marshall, A. G.; Mathews, J. P. Fuel 2012, 95, 35-49
13. Marshall, A.; Blakney, G.; Beu, S.; Hendrickson, C.; McKenna, A.; Purcell, J.; Rodgers, R.; Xian, F. Eur. J. Mass Spectrom. 2010, 16, 367-371
14. Nagels, L. J.; Creten, W. L.; Vanpeperstraete, P. M. Anal. Chem. 1983, 55, 216-220
15. Ricard, E.; Pecheyran, C.; Sanabria Ortega, G.; Prinzhofer, A.; Donard, O. X. Anal. Bioanal. Chem. 2011, 399, 2153-2165
16. Swearingen, K. E.; Hoopmann, M. R.; Johnson, R. S.; Saleem, R. A.; Aitchison, J. D.; Moritz, R. L. Mol. Cell. Proteomics 2012, 11, M111.014985
17. Liu, H.; Sadygov, R. G.; Yates, J. R. Anal. Chem. 2004, 76, 4193-4201
18. Jmeian, Y.; El Rassi, Z. Electrophoresis 2009, 30, 249-261
19. Corthals, G. L.; Wasinger, V. C.; Hochstrasser, D. F.; Sanchez, J.-C. Electrophoresis 2000, 21, 1104-1115
20. Eriksson, J.; Fenyö, D. J. Proteome Res. 2005, 4, 387-393
21. Southam, A. D.; Payne, T. G.; Cooper, H. J.; Arvanitis, T. N.; Viant, M. R. Anal. Chem. 2007, 79, 4595-4602
22. Becker, S.; Kortz, L.; Helmschrodt, C.; Thiery, J.; Ceglarek, U. J. Chromatogr., B 2012, 883-884, 68-75
23. Wong, C. L.; Cociorva, D.; Venable, J. D.; Xu, T.; Yates, J. R. J. Am. Soc. Mass Spectrom. 2009, 20, 1405-1414
24. Riedo, A.; Bieler, A.; Neuland, M.; Tulej, M.; Wurz, P. J. Mass Spectrom. 2013, 48, 1-15
25. Xian, F.; Corilo, Y. E.; Hendrickson, C. L.; Marshall, A. G. Int. J. Mass Spectrom. 2012, 325-327, 67-72
26. Jungmann, J. H.; MacAleese, L.; Visser, J.; Vrakking, M. J. J.; Heeren, R. M. A. Anal. Chem. 2011, 83, 7888-7894
27. Abplanalp, D.; Wurz, P.; Huber, L.; Leya, I. Int. J. Mass Spectrom. 2010, 294, 33-39
28. Belov, M. E.; Anderson, G. A.; Angell, N. H.; Shen, Y.; Tolic, N.; Udseth, H. R.; Smith, R. D. Anal. Chem. 2001, 73, 5052-5060
29. Kaiser, N. K.; McKenna, A. M.; Savory, J. J.; Hendrickson, C. L.; Marshall, A. G. Anal. Chem. 2013, 85, 265-272
30. Kilgour, D. P. A.; Mackay, C. L.; Langridge-Smith, P. R. R.; O'Connor, P. B. Anal. Chem. 2012, 84, 7431-7435
31. Senko, M.; Beu, S.; McLafferty, F. J. Am. Soc. Mass Spectrom. 1995, 6, 52-56
32. Fornelli, L.; Parra, J.; Hartmer, R.; Stoermer, C.; Lubeck, M.; Tsybin, Y. Anal. Bioanal. Chem. 2013, 405, 8505-8514
33. Liu, X.; Inbar, Y.; Dorrestein, P. C.; Wynne, C.; Edwards, N.; Souda, P.; Whitelegge, J. P.; Bafna, V.; Pevzner, P. A. Mol. Cell. Proteomics 2010, 9, 2772-2782
34. Klitzke, C. F.; Corilo, Y. E.; Siek, K.; Binkley, J.; Patrick, J.; Eberlin, M. N. Energy Fuels 2012, 26, 5787-5794
35. Schramm, T.; Hester, A.; Klinkert, I.; Both, J.-P.; Heeren, R. M. A.; Brunelle, A.; Laprévote, O.; Desbenoit, N.; Robbe, M.-F.; Stoeckli, M.; Spengler, B.; Römpp, A. J. Proteomics 2012, 75, 5106-5110
36. McKenna, A. M.; Donald, L. J.; Fitzsimmons, J. E.; Juyal, P.; Spicer, V.; Standing, K. G.; Marshall, A. G.; Rodgers, R. P. Energy Fuels 2013, 27, 1246-1256
37. Wilhelm, M.; Kirchner, M.; Steen, J. A. J.; Steen, H. Mol. Cell. Proteomics 2012, 11, O111.011379
38. Ben Hamidane, H.; Vorobyev, A.; Tsybin, Y. O. Eur. J. Mass Spectrom. 2011, 17, 321-331
39. Fornelli, L.; Damoc, E.; Thomas, P. M.; Kelleher, N. L.; Aizikov, K.; Denisov, E.; Makarov, A.; Tsybin, Y. O. Mol. Cell. Proteomics 2012, 11, 1758-1767
40. The open-source release is available at https://bitbucket.org/kozhinov/ pyftms.
41. Smith, D. F.; Schaub, T. M.; Rodgers, R. P.; Hendrickson, C. L.; Marshall, A. G. Anal. Chem. 2008, 80, 7379-7382
42. Purcell, J. M.; Hendrickson, C. L.; Rodgers, R. P.; Marshall, A. G. Anal. Chem. 2006, 78, 5906-5912
43. Shi, Q.; Zhao, S.; Xu, Z.; Chung, K. H.; Zhang, Y.; Xu, C. Energy Fuels 2010, 24, 4005-4011
44. Liao, Y.; Shi, Q.; Hsu, C. S.; Pan, Y.; Zhang, Y. Org. Geochem. 2012, 47, 51-65
45. Hsu, C.-S.; Hendrickson, C. L.; Rodgers, R. P.; McKenna, A. M.; Marshall, A. G. J. Mass Spectrom. 2011, 46, 337-343
46. Chiaberge, S.; Fiorani, T.; Savoini, A.; Bionda, A.; Ramello, S.; Pastori, M.; Cesti, P. Fuel Process. Technol. 2013, 106, 181-185
47. Marshall, A. G.; Hendrickson, C. L. Annu. Rev. Anal. Chem. 2008, 1, 579-599
48. Podgorski, D. C.; Corilo, Y. E.; Nyadong, L.; Lobodin, V. V.; Robbins, W. K.; McKenna, A. M.; Marshall, A. G.; Rodgers, R. P. Energy Fuels 2013, 27, 1268-1276
49. McAlister, G. C.; Berggren, W. T.; Griep-Raming, J.; Horning, S.; Makarov, A.; Phanstiel, D.; Stafford, G.; Swaney, D. L.; Syka, J. E. P.; Zabrouskov, V.; Coon, J. J. J. Proteome Res. 2008, 7, 3127-3136
50. Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332
51. Purvine, S.; Kolker, N.; Kolker, E. OMICS 2004, 8, 255-265
52. Xu, H.; Freitas, M. A. BMC Bioinf. 2010, 11, 436
53. Wu, C.; Qian, K.; Nefliu, M.; Cooks, R. G. J. Am. Soc. Mass Spectrom. 2010, 21, 261-267
54. Guan, S.; Burlingame, A. L. J. Am. Soc. Mass Spectrom. 2010, 21, 455-459
55. Sun, L.; Knierman, M. D.; Zhu, G.; Dovichi, N. J. Anal. Chem. 2013, 85, 5989-5995
56. Lange, O. Methods and Apparatus for Producing a Mass Spectrum. U.S. Patent 20110240841, 2011.
57. Lange, O.; Damoc, E.; Wieghaus, A.; Makarov, A. Proceedings of the 59th ASMS Conference on Mass Spectrometry and Allied Topics, Denver, CO, USA, June 5-9, 2011.
58. Kekäläinen, T.; Pakarinen, J. M. H.; Wickström, K.; Lobodin, V. V.; McKenna, A. M.; Jänis, J. Energy Fuels 2013, 27, 2002-2009
59. Zubarev, R. A. Proteomics 2013, 13, 723-726
60. Hughey, C. A.; Hendrickson, C. L.; Rodgers, R. P.; Marshall, A. G.; Qian, K. Anal. Chem. 2001, 73, 4676-4681
61. Kozhinov, A. N.; Miladinovic, S. M.; Tsybin, Y. O. Proceedings of the 59th ASMS Conference on Mass Spectrometry and Allied Topics, Denver, CO, USA, June 5-9, 2011.
62. Kozhinov, A. N.; Zhurov, K. O.; Tsybin, Y. O. Anal. Chem. 2013, 85, 6437-6445
63. Bendat, J. S.; Piersol, A. G. Random Data: Analysis and Measurement Procedures, 4 th ed.; Wiley: Hoboken, NJ, 2010; p 640.