A fast and accurate algorithm for the quantification of peptides from mass spectrometry data

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4453 LNBI, Issue , 2007, Pages 473-487

  Schulz Trieglaff, Ole ^a,b   Hussong, Rene ^c   Gröpl, Clemens ^b   Hildebrandt, Andreas ^c   Reinert, Knut ^b  

^a Max Planck Research School   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES; WAVELET ANALYSIS;

COMPUTATIONAL TOOLS; RAW INSTRUMENT DATA;

ALGORITHMS;

EID: 34547411379     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-71681-5_33     Document Type: Conference Paper

References (28)

1. M. Bellew, M. Coram, M. Fitzgibbon, M. Igra, T. Randolph, P. Wang, D. May, J. Eng, R. Fang, C-W. Lin, J. Chen, D. Goodlett, J. Whiteaker, A. Paulovich, and M. McIntosh. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics, 22(15):1902-1909, 2006.
2. J.L. Bentley and T. Ottmann. Algorithms for reporting and counting geometric intersections. IEEE Trans. Comput, 028:643-647, 1979.
3. Valerio B. Di Marco and G. Giorgio Bombi, Mathematical functions for the representation of chromatographic peaks. Journal of Chromatography A, 931:1-30, 2001.
4. Pan Du, Warren A. Kibbe, and Simon M. Lin, Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics, 22:2059 - 2065, 2006.
5. B. Fischer, J. Grossmann, V. Roth, and W. Gruissem. Semi-supervised LC/MS alignment for differential proteomics. Bioinformatics, 22:e132-e140, 2006.
6. C. Gröpl, E. Lange, K. Reinert, O. Kohlbacher, M. Sturm, CG. Huber, B. Mayr, and C. Klein. Algorithms for the automated absolute quantification of diagnostic markersin complex proteomics samples. In Michael Berthold, editor, Procceedings of CompLife 2005, Lecture Notes in Bioinformatics, pages 151-163. Springer, Heidelberg, 2005.
7. David M. Horn, Roman A. Zubarev, and Fred W. McLafferty. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. Journal of the American Society for Mass Spectrometry, 11(4):320-332, April 2000. Seminal paper on quantification of peptides of high-resolution spectra.
8. A. Keller, A. Nesvizhskii, E. Kolker, and R. Aebersold. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem., 74:5383-5392, 2002,
9. O. Kohlbacher, K. Reinert, C. Gröpl, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, and M. Sturm. TOPP - The OpenMS proteomics pipeline. In Proceedings of the 5th European Conference on Computational Biology (accepted), 2006.
10. H. Kubinyi. Calculation of isotope distributions in mass spectrometry, a trivial solution for a non-trivial problem. Anal. Chim. Acta, 247:107-119, 1991.
11. E. Lange, C. Gröpl, K. Reinert, O. Kohlbacher, and A. Hildebrandt. High accuracy peak-picking of proteomics data using wavelet techniques. In Proceedings of the Pacific Symposium on Biocomputing (PSB) 2006, pages 243-254, 2006.
12. K.C. Leptos, D.A. Sarracino, J.D. Jaffe, B. Krastins, and G.M. Church. MapQuant: Open-Source software for large-scale protein quantification. Proteomics, 6(6):1770-1782, 2006.
13. K. Levenberg. A method for the solution of certain problems in least squares. Quart. Appl. Math., 2:164-168, 1944.
14. H. Li, X.-J.and Zhang, J.R. Ranish, and R. Aebersold. Automated statistical analysis of protein abundance ratios from data generated by stable isotope dilution and tandem mass spectrometry. Anal. Chem., 75:6648-6657, 2003.
15. X.-J. Li, E.C. Yi, C.J. Kemp, H. Zhang, and R. Aebersold, A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol. Cell Proteomics, 4(9):1328-1340, 2005.
16. J. Listgarten and A. Emili. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics, 4(4):419-434, 2005.
17. M.J. MacCoss and D.E. Matthews, Quantitative MS for proteomics: Teaching a new dog old tricks. Anal. Chem., 77(15):294A-302A., 2005.
18. M. Mann and R. Aebersold. Mass spectrometry-based proteomics. Nature 422, 422:198 - 207, 2003.
19. D. Marquardt. An algorithm for least-squares estimation of nonlinear parameters. SIAM J. Appl. Math., 11:431-441, 1963.
20. B.M. Mayr, O. Kohlbacher, K. Reinert, M. Sturm, C Gröpl, E. Lange, C Klein, and C Huber. Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. J. Proteome Res., 5:414-421, 2006.
21. S.-E. Ong and M. Mann. Mass spectrometry-based proteomics turns quantitative, Nature Chem. Biology, 1(5):252-262, 2005.
22. P.M. Palagi, P. Hernandez, D. Walther, and R.D. Appel. Proteome informatics I: Bioinformatics tools for processing experimental data. Proteomics, ISSN 1615-9861, http://dx.doi.org/10.1002/pmic.200600273 (epub ahead of print), 2006.
23. Tomas Rejtar, Hsuan shen Chen, Victor Andreev, Eugene Moskovets, and Barry L. Karger. Increased identification of peptides by enhanced data processing of high-resolution maldi tof/tof mass spectra prior to database searching. Analytical Chemistry, 76:6017 -6028, 2004.
24. A.L. Rockwood, S.L. Van Orden, and R.D. Smith. Rapid calculation of isotope distributions. Analytical Chemistry, 67:269972704, 1995.
25. M.W. Senko, S.C. Beu, and F.W. McLafferty. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. Journal of the American Society for Mass Spectrometry, 6(4):229-233, 1995.
26. CA. Smith, E.J. Want, G. O'Maille, R. Abagyan, and G. Siuzdak. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Analytical Chemistry, 78(3):779-787, 2006.
27. G. Wang, W.W. Wu, T. Pisitkun, J.D. Hoffert, M.A. Knepper, and R.-F. Shen. Automated quantification tool for high-throughput proteomics using stable isotope labeling and LC-MS. Analytical Chemistry, 78(16):5752-5761, 2006.
28. J.A. Yergey. A general approach to calculating isotopic distributions for mass spectrometry. Int. J. Mass Spectrom. Ion Phys., 52:3377349, 1987.