De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra

peer-reviewed · Journal of Proteome Research · 2014

peer-reviewed · Journal of Proteome Research · 2014. Xiaowen Liu et al. There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS)…

Date	2014-07-03
Type	peer-reviewed
Venue	Journal of Proteome Research
Publisher	American Chemical Society (ACS)
Contribution	algorithm
DOI	10.1021/pr401300m
Citations (OpenAlex)	72
Venue 2-year citedness	3.83

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.

Authors

1. Xiaowen Liu · Indiana University Indianapolis, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, Tulane University, University of Waterloo
2. Lennard J. M. Dekker · Erasmus MC, Erasmus University Rotterdam
3. Si Wu · Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, University of Oklahoma
4. Martijn M. VanDuijn · Erasmus MC, Erasmus University Rotterdam
5. Theo M. Luider · Erasmus MC, Erasmus University Rotterdam
6. Nikola Tolić · Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
7. Qiang Kou · Indiana University-Purdue University Indianapolis
8. Mikhail Dvorkin · Saint Petersburg Academic University, Saint Petersburg National Research Academic University of the Russian Academy of Sciences
9. Sonya Alexandrova · Saint Petersburg Academic University, Saint Petersburg National Research Academic University of the Russian Academy of Sciences
10. Kira Vyatkina · ITMO University, Saint Petersburg Academic University, Saint Petersburg National Research Academic University of the Russian Academy of Sciences, Saint Petersburg State Electrotechnical University, St Petersburg University, St. Petersburg State University
11. Ljiljana Paša-Tolić · Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
12. Pavel A. Pevzner · Max Planck Institute of Molecular Cell Biology and Genetics, Saint Petersburg Academic University, St Petersburg University, St. Petersburg State University, University of California San Diego, University of Southern California

Methods and tools

• Top-down plus bottom-up de novo protein sequencing: Uses top-down spectra of the intact protein as a scaffold to assemble bottom-up de novo peptide reads into a full protein sequence.

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