vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RASvavilov-328Research ArticleСтатьиArticlesВОССТАНОВЛЕНИЕ АМИНОКИСЛОТНОЙ ПОСЛЕДОВАТЕЛЬНОСТИ ЦИКЛИЧЕСКИХ ПЕПТИДОВ ИЗ МАСС-СПЕКТРОВRECONSTRUCTION OF AMINO ACID SEQUENCES OF CYCLIC PEPTIDES FROM THEIR MASS SPECTRAФоминЭ. С.FominE. S.fomin@bionet.nsc.ruФедеральное государственное бюджетное научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук», Новосибирск, РоссияРоссияInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaRussian Federation201422012015184/2973982Copyright © Фомин Э.С., 20152015Фомин Э.С.Fomin E.S.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/328

Метод масс-спектрометрии −один из физических методов исследования протеомов различных организмов, позволяющий решать как задачи идентификации биологических макромолекул, так и секвенирования пептидных цепочек в случаях, когда нет информации о геномах либо эта информация крайне ограничена. В настоящее время существует множество компьютерных программ для поддержки исследований в этой области. Тем не менее, несмотря на высокую активность, имеется только незначительный прогресс в создании программпозволяющих решать задачи de novo секвенирования для циклических пептидов, к которым относятся наиболее эффективные антибиотики, противоопухолевые агенты, иммунодепрессанты, токсины и множество пептидов с неизвестными функциями, синтезируемые в клетке по нерибосомальному пути. Предложен эффективный алгоритм для решения задачи секвенирования циклических пептидов, который позволяет восстанавливать последовательности большой (до 160 аминокислотных остатков) длины.

Mass spectrometry is a physical method, which can be applied to the investigation of proteomes of different organisms. It allows us both to solve the problem of identification of biological macromolecules and to sequence peptide chains in cases where information on the genomes is scarce or absent. Currently, there are many software programs to support research in this area. Nevertheless, in spite of all efforts, there is little progress in the development of programs able to solve the problem for de novo sequencing of cyclic peptides, which are most effective antibiotics, antitumor agents, immunosuppressants, toxins, and a vast number of nonribosomal peptides with unknown functions. In this paper, an effective algorithm for solving the problem of de novo sequencing cyclic peptides is proposed. The algorithm allows us to reconstruct sequences of lengths up to 160 amino acid residues.

масс-спектрометриясеквенирование циклических пептидовпроблема beltwaymass spectrometrysequencing of cyclic peptidesbeltway problemСО РАНReferencesОстерман Л.А. Методы исследования белков и нуклеиновых кислот: электрофорез и ультрацентрифугирование. М.: Наука, 1981. 286 c.Остерман Л.А. Методы исследования белков и нуклеиновых кислот: электрофорез и ультрацентрифугирование. М.: Наука, 1981. 286 c.Aebersold R., Mann M. Mass spectrometry-based proteomics // Nature. 2003. V. 422. P. 198−207.Aebersold R., Mann M. Mass spectrometry-based proteomics // Nature. 2003. V. 422. P. 198−207.Allison L., Yee C.N. Restriction site mapping is in separation theory // Comput. Appl. Biol. Sci. 1988. V. 4. P. 97–101.Allison L., Yee C.N. Restriction site mapping is in separation theory // Comput. Appl. Biol. Sci. 1988. V. 4. P. 97–101.Allmer J. Algorithms for the de novo sequencing of peptides from tandem mass spectra // Expert Review of Proteomics. 2011. V. 8. No. 5. P. 645–657.Allmer J. Algorithms for the de novo sequencing of peptides from tandem mass spectra // Expert Review of Proteomics. 2011. V. 8. No. 5. P. 645–657.Benjamini Y., Hochberg Y. Controlling the false discovery rate – a practical and powerful approach to multiple testing // J. R. Stat. Soc. Ser. B. Methodol. 1995. V. 57. P. 289–300.Benjamini Y., Hochberg Y. Controlling the false discovery rate – a practical and powerful approach to multiple testing // J. R. Stat. Soc. Ser. B. Methodol. 1995. V. 57. P. 289–300.Chen T., Kao M., Tepel M., Rush J., Church G.M. A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry // Proc. of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). San Francisco. CA. 2000. P. 389–398.Chen T., Kao M., Tepel M., Rush J., Church G.M. A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry // Proc. of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). San Francisco. CA. 2000. P. 389–398.Clauser K.R., Baker P., Burlingame A.L. Role of accurate mass measurement (+/-10 ppm) in protein identifi cation strategies employing MS or MS/MS and database searching // Anal. Chem. 1999. V. 71. P. 2871–2882.Clauser K.R., Baker P., Burlingame A.L. Role of accurate mass measurement (+/-10 ppm) in protein identifi cation strategies employing MS or MS/MS and database searching // Anal. Chem. 1999. V. 71. P. 2871–2882.Colinge J., Masselot A., Giron M. et al. OLAV: Towards highthroughput tandem mass spectrometry data identifi cation // Proteomics. 2003. V. 3. P. 1454–1463.Colinge J., Masselot A., Giron M. et al. OLAV: Towards highthroughput tandem mass spectrometry data identifi cation // Proteomics. 2003. V. 3. P. 1454–1463.Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra // Bioinformatics. 2004. V. 20. P. 1466–1467.Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra // Bioinformatics. 2004. V. 20. P. 1466–1467.Craig R., Cortens J.P., Beavis R.C. The use of proteotypic peptide libraries for protein identification // Rapid Commun. Mass Spectrom. 2005. V. 19. P. 1844–1850.Craig R., Cortens J.P., Beavis R.C. The use of proteotypic peptide libraries for protein identification // Rapid Commun. Mass Spectrom. 2005. V. 19. P. 1844–1850.Craig R., Cortens J.C., Fenyo D., Beavis R.C. Using annotated peptide mass spectrum libraries for protein identifi cation // J. Proteome Res. 2006. V. 5. P. 1843–1849.Craig R., Cortens J.C., Fenyo D., Beavis R.C. Using annotated peptide mass spectrum libraries for protein identifi cation // J. Proteome Res. 2006. V. 5. P. 1843–1849.Dainty J.C., Fienup J.R. Phase Retrieval and Image Reconstruction for Astronomy. Image Recovery: Theory and Application, 1987. P. 231–275.Dainty J.C., Fienup J.R. Phase Retrieval and Image Reconstruction for Astronomy. Image Recovery: Theory and Application, 1987. P. 231–275.Dakic T. On the Turnpike Problem. PhD Thesis. Simon Fraser University, 2000.Dakic T. On the Turnpike Problem. PhD Thesis. Simon Fraser University, 2000.Dančík V., Addona T.A., Clauser K.R., Vath J.E., Pevzner P.A. De Novo Peptide Sequencing via Tandem Mass Spectrometry // J. Computational Biology. 1999. V. 6. No. 3-4. P. 327–342.Dančík V., Addona T.A., Clauser K.R., Vath J.E., Pevzner P.A. De Novo Peptide Sequencing via Tandem Mass Spectrometry // J. Computational Biology. 1999. V. 6. No. 3-4. P. 327–342.Elias J.E., Gygi, S.P. Target-decoy search strategy for increased confi dence in large-scale protein identifi cations by mass spectrometry // Nat. Methods. 2007. V. 4. P. 207–214.Elias J.E., Gygi, S.P. Target-decoy search strategy for increased confi dence in large-scale protein identifi cations by mass spectrometry // Nat. Methods. 2007. V. 4. P. 207–214.Eng J.K., McCormack A.L., Yates J.R. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database // J. Am. Soc. Mass Spectrom. 1994. V. 5. P. 976–989.Eng J.K., McCormack A.L., Yates J.R. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database // J. Am. Soc. Mass Spectrom. 1994. V. 5. P. 976–989.Frank A., Pevzner P. PepNovo: de novo peptide sequencing via probabilistic network modeling // Anal. Chem. 2005. V. 77. P. 964–973.Frank A., Pevzner P. PepNovo: de novo peptide sequencing via probabilistic network modeling // Anal. Chem. 2005. V. 77. P. 964–973.Frewen B.E., Merrihew G.E., Wu C. et al. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries // Anal. Chem. 2006. V. 78. P. 5678–5684.Frewen B.E., Merrihew G.E., Wu C. et al. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries // Anal. Chem. 2006. V. 78. P. 5678–5684.Hubbard S.J., Jones A.R. Proteome Bioinformatics. Humana Press, 2010.Hubbard S.J., Jones A.R. Proteome Bioinformatics. Humana Press, 2010.Jaganathan K., Hassibi B. Reconstruction of Integers from Pairwise Distances // Acoustics, Speech and Signal Processing (ICASSP). IEEE International Conference. 2013. P. 5974–5978.Jaganathan K., Hassibi B. Reconstruction of Integers from Pairwise Distances // Acoustics, Speech and Signal Processing (ICASSP). IEEE International Conference. 2013. P. 5974–5978.Jaganathan K., Oymak S., Hassibi B. Sparse phase retrieval: Uniqueness guarantees and recovery algorithms. arXiv:1311.2745 [cs, math], Nov. 2013. [Online]. Available: http://arxiv.org/abs/1311.2745.Jaganathan K., Oymak S., Hassibi B. Sparse phase retrieval: Uniqueness guarantees and recovery algorithms. arXiv:1311.2745 [cs, math], Nov. 2013. [Online]. Available: http://arxiv.org/abs/1311.2745.Johnson R.S., Taylor J.A. Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry // Mol. Biotechnol. 2002. V. 22. P. 301–315.Johnson R.S., Taylor J.A. Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry // Mol. Biotechnol. 2002. V. 22. P. 301–315.Keller A., Nesvizhskii A.I., Kolker E., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifi cations made by MS/MS and database search // Anal. Chem. 2002. V. 74. P. 5383–5392.Keller A., Nesvizhskii A.I., Kolker E., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifi cations made by MS/MS and database search // Anal. Chem. 2002. V. 74. P. 5383–5392.Lambert B., Jacques V., Shivanyuk A. et al. Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide (III) and thorium (IV) complexes // Inorg. Chem. 2000. V. 39. No. 10. P. 2033−2041.Lambert B., Jacques V., Shivanyuk A. et al. Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide (III) and thorium (IV) complexes // Inorg. Chem. 2000. V. 39. No. 10. P. 2033−2041.Lemke P., Skiena S.S., Smith W.D. Reconstructing Sets From Interpoint Distances // Discrete Computational Geometry Algorithms Combinatorics. 2003. V. 25. P. 597–631.Lemke P., Skiena S.S., Smith W.D. Reconstructing Sets From Interpoint Distances // Discrete Computational Geometry Algorithms Combinatorics. 2003. V. 25. P. 597–631.Lide D.R. Handbook of Chemistry and Physics. 72nd Ed. CRC Press. Boca Raton. FL., 1991.Lide D.R. Handbook of Chemistry and Physics. 72nd Ed. CRC Press. Boca Raton. FL., 1991.Ma B., Zhang K., Hendrie C. et al. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry // Rapid Commun. Mass Spectrom. 2003. V. 17. P. 2337–2342.Ma B., Zhang K., Hendrie C. et al. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry // Rapid Commun. Mass Spectrom. 2003. V. 17. P. 2337–2342.Marahiel M.A., Nakano M.M., Zuber P. Regulation of peptide antibiotic production in Bacillus // Mol Microbiol. 1993. V. 7. No. 5. P. 631–636.Marahiel M.A., Nakano M.M., Zuber P. Regulation of peptide antibiotic production in Bacillus // Mol Microbiol. 1993. V. 7. No. 5. P. 631–636.Millane R.P. Phase retrieval in crystallography and optics // J. Opt. Soc. Am. A. 1990. V. 7. No. 3. P. 394–411.Millane R.P. Phase retrieval in crystallography and optics // J. Opt. Soc. Am. A. 1990. V. 7. No. 3. P. 394–411.Mohimani H., Liu W.T., Yang Y.L. et al. Multiplex De Novo Sequen-cing of Peptide Antibiotics // J. Comp. Biol. 2011. V. 18. No. 11. P. 1371–1381.Mohimani H., Liu W.T., Yang Y.L. et al. Multiplex De Novo Sequen-cing of Peptide Antibiotics // J. Comp. Biol. 2011. V. 18. No. 11. P. 1371–1381.Nesvizhskii A.I., Vitek O., Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry // Nature methods. 2007. V. 4. No. 10. P. 787–797.Nesvizhskii A.I., Vitek O., Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry // Nature methods. 2007. V. 4. No. 10. P. 787–797.Ng J., Bandeira N., Liu W. et al. Dereplication and de novo sequencing of nonribosomal peptides // Nat. Methods. 2009. V. 6. P. 596–599.Ng J., Bandeira N., Liu W. et al. Dereplication and de novo sequencing of nonribosomal peptides // Nat. Methods. 2009. V. 6. P. 596–599.Pandurangan G., Ramesh H. The restriction mapping problem revisited // J. Computer System Sciences. 2002. V. 65. P. 526–544.Pandurangan G., Ramesh H. The restriction mapping problem revisited // J. Computer System Sciences. 2002. V. 65. P. 526–544.Pappin D.J.C., Hojrup P., Bleasby A.J. Rapid identifi cation of proteins by peptide-mass fi ngerprinting Transportable // Current Biology. 1993. V. 3. P. 327−332.Pappin D.J.C., Hojrup P., Bleasby A.J. Rapid identifi cation of proteins by peptide-mass fi ngerprinting Transportable // Current Biology. 1993. V. 3. P. 327−332.Perkins D.N., Pappin D.J.C., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data // Electrophoresis. 1999. V. 20. P. 3551–3567.Perkins D.N., Pappin D.J.C., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data // Electrophoresis. 1999. V. 20. P. 3551–3567.Rabiner L., Juang B.H. Fundamentals of Speech Recognition. Signal Processing Series. Prentice Hall. 1993.Rabiner L., Juang B.H. Fundamentals of Speech Recognition. Signal Processing Series. Prentice Hall. 1993.Rahn J. Possible and impossible melodies: Some formal aspects of contour // Journal Music Theory. 1994. V. 36. No. 2. P. 259–279.Rahn J. Possible and impossible melodies: Some formal aspects of contour // Journal Music Theory. 1994. V. 36. No. 2. P. 259–279.Shamos M.I. Problems in computational geometry. CMU. Pittsburgh. PA, 1977.Shamos M.I. Problems in computational geometry. CMU. Pittsburgh. PA, 1977.Sieber S., Marahiel M. Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics // Chem. Rev. 2005. V. 105. P. 715–738.Sieber S., Marahiel M. Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics // Chem. Rev. 2005. V. 105. P. 715–738.Skiena S.S., Smith W.D., Lemke P. Reconstructing sets from interpoint distances // Proc. Sixth ACM Symposium Computational Geometry. Berkeley. CA, 1990. P. 332–339.Skiena S.S., Smith W.D., Lemke P. Reconstructing sets from interpoint distances // Proc. Sixth ACM Symposium Computational Geometry. Berkeley. CA, 1990. P. 332–339.Stefik M. Inferring DNA structures from segmentation data // Artif. Intell. 1978. V. 11. P. 85–114.Stefik M. Inferring DNA structures from segmentation data // Artif. Intell. 1978. V. 11. P. 85–114.Storey J.D., Tibshirani R. Statistical signifi cance for genomewie studies // Proc. Natl. Acad. Sci. USA. 2003. V. 100. P. 9440–9445.Storey J.D., Tibshirani R. Statistical signifi cance for genomewie studies // Proc. Natl. Acad. Sci. USA. 2003. V. 100. P. 9440–9445.Walther A. The question of phase retrieval in optics // Opt. Acta. 1963. V. 10. P. 41–49.Walther A. The question of phase retrieval in optics // Opt. Acta. 1963. V. 10. P. 41–49.Wuthrich K. NMR of Proteins and Nucleic Acids. John Wiley and Sons. N. Y., 1986.Wuthrich K. NMR of Proteins and Nucleic Acids. John Wiley and Sons. N. Y., 1986.Zhang N., Aebersold R., Schwilkowski B. ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data // Proteomics. 2002. V. 2. P. 1406–1412.Zhang N., Aebersold R., Schwilkowski B. ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data // Proteomics. 2002. V. 2. P. 1406–1412.

The authors declare that there are no conflicts of interest present.