An efficient method to calculate the aggregated isotopic distribution and exact center-masses

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 4, 2012, Pages 753-763

  Claesen, Jürgen ^a   Dittwald, Piotr ^b,c   Burzykowski, Tomasz ^a   Valkenborg, Dirk ^a,d,e  

^a HASSELT UNIVERSITY   (Belgium)

^b UNIVERSITY OF WARSAW   (Poland)

^c UNIVERSITY OF WARSAW   (Poland)

^d FLEMISH INSTITUTE FOR TECHNOLOGICAL RESEARCH VITO   (Belgium)

^e UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

Accurate mass; Isotopic distribution; Mass spectrometry; Metabolomics; Proteomics

Indexed keywords

ACCURATE MASS; ATOMIC COMPOSITIONS; ISOTOPIC DISTRIBUTIONS; MASS CENTERS; MATHEMATICAL PROPERTIES; METABOLOMICS; NATURAL ABUNDANCE; PROTEOMICS;

AGGREGATES; BIOMOLECULES; MASS SPECTROMETRY; MERCURY (METAL); MOLECULES; PROBABILITY DISTRIBUTIONS;

ISOTOPES;

ABC TRANSPORTER; ADENOSINE TRIPHOSPHATASE (POTASSIUM SODIUM); ANGIOTENSIN II; BOVINE INSULIN; BOVINE SERUM ALBUMIN; DYNEIN ADENOSINE TRIPHOSPHATASE; HUMAN INSULIN; HYDROXOCOBALAMIN; INTRINSIC FACTOR; ISOTOPE; MYOGLOBIN;

AGGREGATED ISOTOPIC DISTRIBUTION; ALGORITHM; ARTICLE; BAFFLING RECURSIVE ALGORITHM FOR ISOTOPIC DISTRIBUTION CALCULATIONS; CALCULATION; CHEMICAL COMPOSITION; COMPUTER PROGRAM; CONTROLLED STUDY; EXACT CENTER MASS; MASS; MASS SPECTROMETRY; MATHEMATICAL PHENOMENA; MOLECULE; PROBABILITY;

ALGORITHMS; ANIMALS; CATTLE; HUMANS; ISOTOPES; MASS SPECTROMETRY; MOLECULAR WEIGHT; PROTEINS; SOFTWARE;

EID: 84862557848     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-011-0326-2     Document Type: Article

References (26)

1. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A.J., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, J.Y.H., Zhang, J.: Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)
2. Breen, E.J., Hopwood, F.G., Williams, K.L., Wilkins, M.R.: Automatic Poisson peak harvesting for high throughput protein identification. Electrophoresis 21, 2243-2251 (2000)
3. Gay, S., Binz, P., Hochstrasser, D., Appel, R.: Modeling peptide mass fingerprinting data using the atomic composition of peptides. Electrophoresis 20, 3527-3534 (1999)
4. Senko, M.W., Beu, S.C., McLafferty, F.W.: Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distribution. J. Am. Soc. Mass Spectrom. 6, 229-233 (1995)
5. Valkenborg, D., Assam, P., Thomas, G., Krols, L., Kas, K., Burzykowski, T.: Using a Poisson approximation to predict the isotopic distribution of sulphur-containing peptides in a peptide-centric proteomic approach. Rapid Commun. Mass Spectrom. 21, 3387-3391 (2007)
6. Valkenborg, D., Jansen, I., Burzykowski, T.: A model-based method for the prediction of the isotopic distribution of peptides. J. Am. Soc. Mass Spectrom. 19(5), 703-712 (2008)
7. Biemann, K.: Mass Spectrometry, Organic Chemical Applications. McGraw-Hill, New York (1962)
8. Yamamoto, H., McCloskey, J.A.: Calculations of isotopic distribution in molecules extensively labeled with heavy isotopes. Anal. Chem. 49, 281-283 (1977)
9. Brownawell, M., Fillippo, J.S.: A program for the synthesis of mass spectral isotopic abundances. J. Chem. Educ. 59(8), 663-665 (1982)
10. Yergey, J.A.: A general approach to calculating isotopic distributions for mass spectrometry. Int. J. Mass Spectrom. Ion Phys. 52, 337-349 (1983)
11. Yergey, J.A., Heller, D., Hansen, G., Cotter, R.J., Fenselau, C.: Isotopic distributions in mass spectra of large molecules. Anal. Chem. 55, 353-356 (1983)
12. Rockwood, A.L.: Relationship of Fourier transforms to isotope distribution calculations. Rapid Commun. Mass Spectrom. 9, 103-105 (1995)
13. Valkenborg, D., Mertens, I., Lemière, F., Witters, E., Burzykowsk, T.: The isotopic distribution conundrum. Mass Spectrom. Rev. 31(1), 96-106 (2012)
14. 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)
15. Rockwood, A.L., Van Orden, S.L.: Ultrahigh-speed calculation of isotope distributions. Anal. Chem. 68, 2027-2030 (1996)
16. Rockwood, A.L., Haimi, P.: Efficient calculation of accurate masses of isotopic peaks. J. Am. Soc. Mass Spectrom. 17, 415-419 (2006)
17. 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, 12-21 (2004)
18. Olson, M., Yergey, A.: Calculation of the isotope cluster for polypeptides by probability grouping. J. Am. Soc. Mass Spectrom. 20, 295-302 (2009)
19. Rosman, K.J.R., Taylor, P.D.P.: Isotopic compositions of the elements 1997. Pure Appl. Chem. 70(1), 217-235 (1998)
20. Senko, M.W.: IsoPro computer program 3.0.
21. Snider, R.K.: Efficient calculation of exact mass isotopic distributions. J. Am. Soc. Mass Spectrom. 18, 1511-1515 (2007)
22. Macdonald, I.G.: Symmetric Functions and Hall Polynomials. Clarendon Press; Oxford University Press, Oxford: New York (1979)
23. Beynon, J.H.: Mass Spectrometry and its Applications to Organic Chemistry. Elsevier, New York (1960)
24. Li, L., Karabacak, M., Cobb, J., Wang, Q., Hong, P., Agar, J.: Memoryefficient calculation of the isotopic mass states of a molecule. Rapid Commun. Mass Spectrom. 24, 2689-2696 (2010)
25. Li, L., Kresh, J., Karabacak, M., Cobb, J., Agar, J., Hong, P.: A hierarchical algorithm for calculating the isotopic fine structures of molecules. J. Am. Soc. Mass Spectrom. 19, 1867-1874 (2008)
26. Rockwood, A.L., Van Orden, S.L., Smith, R.D.: Ultrahigh resolution isotope distribution calculations. Rapid Commun. Mass Spectrom. 10, 54-59 (1996)