Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy

Journal of the American Society for Mass Spectrometry

Volumn 25, Issue 1, 2014, Pages 57-70

  Alves, Gelio ^a   Ogurtsov, Aleksey Y ^a   Yu, Yi Kuo ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Accurate mass; Isotopic Distribution; Mass spectrometry; Proteomics

Indexed keywords

ACCURATE MASS; EVALUATION CRITERIA; FOURIER TRANSFORM ALGORITHMS; HIGH RESOLUTION; ISOTOPIC DISTRIBUTION ANALYSIS; ISOTOPIC DISTRIBUTIONS; POLYNOMIAL ALGORITHM; PROTEOMICS;

ALGORITHMS; BENCHMARKING; MASS SPECTROMETRY; MOLECULAR BIOLOGY; POLYNOMIALS; SOFTWARE PACKAGES;

ISOTOPES;

ISOTOPE;

ACCURACY; ALGORITHM; ARTICLE; COMPUTER PROGRAM; FOURIER TRANSFORMATION; MOLECULAR ISOTOPIC DISTRIBUTION; MOLECULAR ISOTOPIC DISTRIBUTION ANALYSIS; MOLECULAR WEIGHT; PARAMETERS; POLYNOMIAL BASED ALGORITHM;

ALGORITHMS; INTERNET; ISOTOPES; MASS SPECTROMETRY; MOLECULAR WEIGHT; PROTEOMICS; SOFTWARE;

EID: 84892636348     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-013-0733-7     Document Type: Article

References (44)

1. Rosman, K.; Taylor, P.: Isotopic compositions of elements 1997. Pure App. Chem. 70, 217-235 (1998)
2. Michener, R.; Lajtha, K.: Stable Isotopes in Ecology and Environmental Science. Wiley-Blackwell, Massachusetts (2007)
3. Becker, G.W.: Stable isotopic labeling of proteins for quantitative proteomic applications. Brief. Funct. Genom. Proteom. 7(5), 371-382 (2008)
4. Yamamoto, H.; McCloskey, J.A.: Calculations of isotopic distribution in molecules extensively labeled with heavy isotopes. Anal. Chem. 49(2), 281-283 (1977)
5. Rockwood, A.L.: Deconvoluting isotopic distributions to evaluate parent/fragment ion relationships. Rapid Commun. Mass Spectrom. 11(3), 241-248 (1997) (Pubitemid 27133995)
6. Gay, S.; Binz, P.A.; Hochstrasser, D.F.; Appel, R.D.: Modeling peptide mass fingerprinting data using the atomic composition of peptides. Electrophoresis 20(18), 3527-3534 (1999) (Pubitemid 30007250)
7. Blank, P.; Sjomeling, C.; Backlund, P.; Yergey, A.: Use of cumulative distribution functions to characterize mass spectra of intact proteins. J. Am. Soc. Mass Spectrom. 13, 40-46 (2002) (Pubitemid 34552622)
8. Goodlett, D.R.; Bruce, J.E.; Anderson, G.A.; Rist, B.; Pasa-Tolic, L.; Fiehn, O.; Smith, R.D.; Aebersold, R.: Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching. Anal. Chem. 72(6), 1112-1118 (2000) (Pubitemid 30163763)
9. Polacco, B.J.; Purvine, S.O.; Zink, E.M.; Lavoie, S.P.; Lipton, M.S.; Summers, A.O.; Miller, S.M.: Discovering mercury protein modifications in whole proteomes using natural isotope distributions observed in liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteom. (2011). doi: 10.1074/mcp.M110.004853
10. Roussis, S.G.; Proulx, R.: Reduction of chemical formulas from the isotopic peak distributions of high-resolution mass spectra. Anal. Chem. 75(6), 1470-1482 (2003) (Pubitemid 36397182)
11. Nikolaev, E.N.; Jertz, R.; Grigoryev, A.; Baykut, G.: Fine structure in isotopic peak distributions measured using a dynamically harmonized Fourier transform ion cyclotron resonance cell at 7 t. Anal. Chem. 84(5), 2275-2283 (2012)
12. Russell, D.H.; Edmondson, R.D.: High-resolution mass spectrometry and accurate mass measurements with emphasis on the characterization of peptides and proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Mass Spectrom. 32, 263-276 (1997) (Pubitemid 27117554)
13. Werlen, R.C.: Effect of resolution on the shape of mass spectra of proteins: some theoretical considerations. Rapid Commun. Mass Spectrom. 8(12), 976-980 (1994)
14. Marshall, A.G.; Hendrickson, C.L.: High-resolution mass spectrometers. Annu. Rev. Anal. Chem. 1(1), 579-599 (2008)
15. Michalski, A.; Damoc, E.; Lange, O.; Denisov, E.; Nolting, D.; Muller, M.; Viner, R.; Schwartz, J.; Remes, P.; Belford, M.; Dunyach, J.J.; Cox, J.; Horning, S.; Mann, M.; Makarov, A.: Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteom. (2012). doi: 10.1074/mcp.O111.013698
16. Valkenborg, D.; Mertens, I.; Lemiere, F.; Witters, E.; Burzykowski, T.: The isotopic distribution conundrum. Mass Spectrom. Rev. 31(1), 96-109 (2012)
17. Olson, M.; Yergey, A.: Calculation of the isotope cluster for polypeptides by probability grouping. J. Am. Soc. Mass Spectrom. 20, 295-302 (2009)
18. Claesen, J.; Dittwald, P.; Burzykowski, T.; Valkenborg, D.: An efficient method to calculate the aggregated isotopic distribution and exact center-masses. J. Am. Soc. Mass Spectrom. 23, 753-763 (2012)
19. Rockwood, A.L.; Van Orden, S.L.; Smith, R.D.: Rapid calculation of isotope distributions. Anal. Chem. 67(15), 2699-2704 (1995)
20. Rockwood, A.L.; Van Orman, J.R.; Dearden, D.V.: Isotopic compositions and accurate masses of single isotopic peaks. J. Am. Soc. Mass Spectrom. 15(1), 12-21 (2004) (Pubitemid 38094320)
21. Rockwood, A.; Haimi, P.: Efficient calculation of accurate masses of isotopic peaks. J. Am. Soc. Mass Spectrom. 17, 415-419 (2006) (Pubitemid 43290200)
22. Senko, M.W.: IsoPro computer program 3.0.
23. Snider, R.: Efficient calculation of exact mass isotopic distributions. J. Am. Soc. Mass Spectrom. 18, 1511-1515 (2007) (Pubitemid 47096797)
24. Rockwood, A.L.; Van Orden, S.L.; Smith, R.D.: Ultrahigh resolution isotope distribution calculations. Rapid Commun. Mass Spectrom. 10(1), 54-59 (1996) (Pubitemid 126784563)
25. Li, L.; Kresh, J.A.; Karabacak, N.M.; Cobb, J.S.; Agar, J.N.; Hong, P.: A hierarchical algorithm for calculating the isotopic fine structures of molecules. J. Am. Soc. Mass Spectrom. 19(12), 1867-1874 (2008)
26. Fernandez-de Cossio, J.: Efficient packing Fourier-transform approach for ultrahigh resolution isotopic distribution calculations. Anal. Chem. 82(5), 1759-1765 (2010)
27. Brownawell, M.L.; San Filippo, J.: Simulation of chemical instrumentation. ii: A program for the synthesis of mass spectral isotopic abundances. J. Chem. Educ. 59(8), 663 (1982)
28. Yergey, J.A.: A general approach to calculating isotopic distributions for mass spectrometry. Int. J. Mass Spectrom. Ion Phys. 52, 337-349 (1983)
29. Rockwood, A.L.: Relationship of Fourier transforms to isotope distribution calculations. Rapid Commun. Mass Spectrom. 9(1), 103-105 (1995)
30. Cooley, J.W.: The rediscovery of the fast Fourier transform algorithm. Mikrochim. Acta 3, 33-45 (1987)
31. Dittwald, P.; Claesen, J.; Burzykowski, T.; Valkenborg, D.; Gambin, A.: BRAIN: a universal tool for high-throughput calculations of the isotopic distribution for mass spectrometry. Anal. Chem. 85(4), 1991-1994 (2013)
32. Rockwood, A.L.; Van Orden, S.L.: Ultrahigh-speed calculation of isotope distributions. Anal. Chem. 68(13), 2027-2030 (1996)
33. Li, L.; Karabacak, N.M.; Cobb, J.S.; Wang, Q.; Hong, P.; Agar, J.N.: Memory-efficient calculation of the isotopic mass states of a molecule. Rapid Commun. Mass Spectrom. 24(18), 2689-2696 (2010)
34. Fernandez-de Cossio Diaz, J.; Fernandez-de Cossio, J.: Computation of isotopic peak center-mass distribution by fourier transform. Anal. Chem. 84(16), 7052-7056 (2012)
35. Fernandez-de Cossio, J.; Gonzalez, L.J.; Satomi, Y.; Betancourt, L.; Ramos, Y.; Huerta, V.; Amaro, A.; Besada, V.; Padron, G.; Minamino, N.; Takao, T.: Isotopica: a tool for the calculation and viewing of complex isotopic envelopes. Nucleic Acids Res. 32(Web Server issue), W674-W678 (2004) (Pubitemid 38997421)
36. Beynon, J.H.: Mass Spectrometry and Its Applications to Organic Chemistry. Elsevier, New York (1960)
37. Kubinyi, H.: Calculation of isotope distributions in mass spectrometry. A trivial solution for a non-trivial problem. Anal. Chim. Acta 247(1), 107-119 (1991)
38. Margrave, J.L.; Polansky, R.B.: Relative abundance calculations for isotopic molecular species. J. Chem. Educ. 39(7), 335 (1962)
39. Bohman, H.: Approximate Fourier analysis of distribution functions. Arkiv Matematik 4, 99-157 (1961)
40. Harris, F.J.: High-resolution spectral analysis with arbitrary spectral centers and arbitrary spectral resolutions. Comput. Electr. Eng. 3(2), 171-191 (1976)
41. Harris, F.: On the use of windows for harmonic analysis with the discrete Fourier transform. Proc. IEEE 66(1), 5-83 (1978)
42. Press, W.H.; Teukolsky, S.A.; Vetterling, W.T.; Flannery, B.P.: Numerical Recipes in C. The Art of Scientific Computing, 2nd edn. Cambridge University Press, New York, NY (1992)
43. Gould, H.: Fibonacci Q. 37(2), 135-140 (1999)
44. Elliott, M.H.; Smith, D.S.; Parker, C.E.; Borchers, C.: Current trends in quantitative proteomics. J. Mass Spectrom. 44(12), 1637-1660 (2009)