De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods

peer-reviewed · PROTEOMICS · 2017

peer-reviewed · PROTEOMICS · 2017. Kira Vyatkina et al. Despite high-resolution mass spectrometers are becoming accessible for more and more laboratories, tandem…
Date 2017-12-01
Type peer-reviewed
Venue PROTEOMICS
Publisher Wiley
Contribution algorithm
DOI 10.1002/pmic.201600321
Citations (OpenAlex) 12

Abstract

Despite high-resolution mass spectrometers are becoming accessible for more and more laboratories, tandem (MS/MS) mass spectra are still often collected at a low resolution. And even if acquired at a high resolution, software tools used for their processing do not tend to benefit from that in full, and an ability to specify a relative mass tolerance in this case often remains the only feature the respective algorithms take advantage of. We argue that a more efficient way to analyze high-resolution MS/MS spectra should be with methods more explicitly accounting for the precision level, and sustain this claim through demonstrating that a de novo sequencing framework originally developed for (high-resolution) top-down MS/MS data is perfectly suitable for processing high-resolution bottom-up datasets, even though a top-down like deconvolution performed as the first step will leave in many spectra at most a few peaks.

Authors

  1. 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
  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. Xiaowen Liu · Indiana University Indianapolis, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, Tulane University, University of Waterloo
  6. Nikola Tolić · Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
  7. Theo M. Luider · Erasmus MC, Erasmus University Rotterdam
  8. Ljiljana Paša-Tolić · Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory

Methods and tools

  • T-Bruijn graph top-down de novo sequencing: De novo sequencing from TOP-DOWN spectra, where the whole protein is fragmented rather than tryptic peptides: derives sequence tags and assembles them through a T-Bruijn graph, evaluated on carbonic anhydrase 2 and an alemtuzumab Fab.

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