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De Novo protein sequencing by combining top-down and bottom-up tandem mass spectra. / Liu, Xiaowen; Dekker, Lennard J.M.; Wu, Si; Vanduijn, Martijn M.; Luider, Theo M.; Tolić, Nikola; Kou, Qiang; Dvorkin, Mikhail; Alexandrova, Sonya; Vyatkina, Kira; Paša-Tolić, Ljiljana; Pevzner, Pavel A.

In: Journal of Proteome Research, Vol. 13, No. 7, 03.07.2014, p. 3241-3248.

Research output: Contribution to journalArticlepeer-review

Harvard

Liu, X, Dekker, LJM, Wu, S, Vanduijn, MM, Luider, TM, Tolić, N, Kou, Q, Dvorkin, M, Alexandrova, S, Vyatkina, K, Paša-Tolić, L & Pevzner, PA 2014, 'De Novo protein sequencing by combining top-down and bottom-up tandem mass spectra', Journal of Proteome Research, vol. 13, no. 7, pp. 3241-3248. https://doi.org/10.1021/pr401300m

APA

Liu, X., Dekker, L. J. M., Wu, S., Vanduijn, M. M., Luider, T. M., Tolić, N., Kou, Q., Dvorkin, M., Alexandrova, S., Vyatkina, K., Paša-Tolić, L., & Pevzner, P. A. (2014). De Novo protein sequencing by combining top-down and bottom-up tandem mass spectra. Journal of Proteome Research, 13(7), 3241-3248. https://doi.org/10.1021/pr401300m

Vancouver

Liu X, Dekker LJM, Wu S, Vanduijn MM, Luider TM, Tolić N et al. De Novo protein sequencing by combining top-down and bottom-up tandem mass spectra. Journal of Proteome Research. 2014 Jul 3;13(7):3241-3248. https://doi.org/10.1021/pr401300m

Author

Liu, Xiaowen ; Dekker, Lennard J.M. ; Wu, Si ; Vanduijn, Martijn M. ; Luider, Theo M. ; Tolić, Nikola ; Kou, Qiang ; Dvorkin, Mikhail ; Alexandrova, Sonya ; Vyatkina, Kira ; Paša-Tolić, Ljiljana ; Pevzner, Pavel A. / De Novo protein sequencing by combining top-down and bottom-up tandem mass spectra. In: Journal of Proteome Research. 2014 ; Vol. 13, No. 7. pp. 3241-3248.

BibTeX

@article{bb631c038dcb436a844830044fcc7b0c,
title = "De Novo protein sequencing by combining top-down and bottom-up tandem mass spectra",
abstract = "There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS). Existing MS-based methods characterize a novel protein by assembling tandem mass spectra of overlapping peptides generated from multiple proteolytic digestions of the protein. Because each tandem mass spectrum covers only a short peptide of the target protein, the key to high coverage protein sequencing is to find spectral pairs from overlapping peptides in order to assemble tandem mass spectra to long ones. However, overlapping regions of peptides may be too short to be confidently identified. High-resolution mass spectrometers have become accessible to many laboratories. These mass spectrometers are capable of analyzing molecules of large mass values, boosting the development of top-down MS. Top-down tandem mass spectra cover whole proteins. However, top-down tandem mass spectra, even combined, rarely provide full ion fragmentation coverage of a protein. We propose an algorithm, TBNovo, for de novo protein sequencing by combining top-down and bottom-up MS. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass spectra are aligned to the scaffold to increase sequence coverage. Experiments on data sets of two proteins showed that TBNovo achieved high sequence coverage and high sequence accuracy.",
author = "Xiaowen Liu and Dekker, {Lennard J.M.} and Si Wu and Vanduijn, {Martijn M.} and Luider, {Theo M.} and Nikola Toli{\'c} and Qiang Kou and Mikhail Dvorkin and Sonya Alexandrova and Kira Vyatkina and Ljiljana Pa{\v s}a-Toli{\'c} and Pevzner, {Pavel A.}",
year = "2014",
month = jul,
day = "3",
doi = "10.1021/pr401300m",
language = "English",
volume = "13",
pages = "3241--3248",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "7",

}

RIS

TY - JOUR

T1 - De Novo protein sequencing by combining top-down and bottom-up tandem mass spectra

AU - Liu, Xiaowen

AU - Dekker, Lennard J.M.

AU - Wu, Si

AU - Vanduijn, Martijn M.

AU - Luider, Theo M.

AU - Tolić, Nikola

AU - Kou, Qiang

AU - Dvorkin, Mikhail

AU - Alexandrova, Sonya

AU - Vyatkina, Kira

AU - Paša-Tolić, Ljiljana

AU - Pevzner, Pavel A.

PY - 2014/7/3

Y1 - 2014/7/3

N2 - There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS). Existing MS-based methods characterize a novel protein by assembling tandem mass spectra of overlapping peptides generated from multiple proteolytic digestions of the protein. Because each tandem mass spectrum covers only a short peptide of the target protein, the key to high coverage protein sequencing is to find spectral pairs from overlapping peptides in order to assemble tandem mass spectra to long ones. However, overlapping regions of peptides may be too short to be confidently identified. High-resolution mass spectrometers have become accessible to many laboratories. These mass spectrometers are capable of analyzing molecules of large mass values, boosting the development of top-down MS. Top-down tandem mass spectra cover whole proteins. However, top-down tandem mass spectra, even combined, rarely provide full ion fragmentation coverage of a protein. We propose an algorithm, TBNovo, for de novo protein sequencing by combining top-down and bottom-up MS. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass spectra are aligned to the scaffold to increase sequence coverage. Experiments on data sets of two proteins showed that TBNovo achieved high sequence coverage and high sequence accuracy.

AB - There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS). Existing MS-based methods characterize a novel protein by assembling tandem mass spectra of overlapping peptides generated from multiple proteolytic digestions of the protein. Because each tandem mass spectrum covers only a short peptide of the target protein, the key to high coverage protein sequencing is to find spectral pairs from overlapping peptides in order to assemble tandem mass spectra to long ones. However, overlapping regions of peptides may be too short to be confidently identified. High-resolution mass spectrometers have become accessible to many laboratories. These mass spectrometers are capable of analyzing molecules of large mass values, boosting the development of top-down MS. Top-down tandem mass spectra cover whole proteins. However, top-down tandem mass spectra, even combined, rarely provide full ion fragmentation coverage of a protein. We propose an algorithm, TBNovo, for de novo protein sequencing by combining top-down and bottom-up MS. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass spectra are aligned to the scaffold to increase sequence coverage. Experiments on data sets of two proteins showed that TBNovo achieved high sequence coverage and high sequence accuracy.

UR - http://www.scopus.com/inward/record.url?scp=84903691273&partnerID=8YFLogxK

U2 - 10.1021/pr401300m

DO - 10.1021/pr401300m

M3 - Article

C2 - 24874765

AN - SCOPUS:84903691273

VL - 13

SP - 3241

EP - 3248

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 7

ER -

ID: 100631086