NIPTL-Novo: Non-isobaric peptide termini labeling assisted peptide de novo sequencing

peer-reviewed · Journal of Proteomics · 2017

peer-reviewed · Journal of Proteomics · 2017. Shen Zhang et al. A simple and effective de novo sequencing strategy assisted by non-isobaric peptide termini labeling…
Date 2017-02-01
Type peer-reviewed
Venue Journal of Proteomics
Publisher Elsevier BV
Contribution adjacent
DOI 10.1016/j.jprot.2016.12.003
Citations (OpenAlex) 2
Venue 2-year citedness 3.02

Abstract

A simple and effective de novo sequencing strategy assisted by non-isobaric peptide termini labeling, NIPTL-Novo, was established. The y-series ions and b-series ions of peptides can be clearly distinguished according to the different mass tags incorporated in N-terminus and C-terminus. This is helpful for improving the accuracy of peptide sequencing and increasing the sequencing speed. For the spectra commonly identified by both de novo sequencing and database searching software (Mascot or Maxquant), NIPTL-Novo gave identical result to more than 85% of these spectra. Furthermore, the quantitative profiling of the sample can be performed simultaneously along with de novo sequencing. Finally, this strategy can be applied to discover the peptides with potential mutation sites by combining with mass-defect based isotopic labeling. Significance The aim of the research presented in this paper is to establish a simple but effective de novo sequencing strategy based on non-isobaric peptide termini labeling, named NIPTL-Novo. First, different mass tags incorporated in N-terminus and C-terminus generated by non-isobaric peptide termini labeling will help to distinguish both b and y ion series, which significantly simplify the MS/MS spectra and reduce the time consumption for de novo sequencing. Second, the isolation window of this strategy is just 4Da, much smaller than most existed labeling assisted de novo sequencing methods, which reduces the interferences caused by co-fragmentation ions. Third, the quantitative profiling of the sample can be performed simultaneously along with the de novo sequencing, and the quantitative accuracy is comparable to other chemical labeling methods. Finally, this strategy was expanded to the analysis of peptide mutation with combination of mass-defect based labeling, and two reliable mutated peptides were discovered.

Authors

  1. Shen Zhang · Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Chinese Academy of Sciences
  2. Yichu Shan · Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Shanghai Institute of Organic Chemistry
  3. Shurong Zhang · Dalian Institute of Chemical Physics, Chinese Academy of Sciences
  4. Zhigang Sui · Dalian Institute of Chemical Physics, Chinese Academy of Sciences
  5. Lihua Zhang · Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Shanghai Institute of Organic Chemistry
  6. Zhen Liang · Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences
  7. Yukui Zhang · Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences

Methods and tools

  • NIPTL-Novo: Non-isobaric peptide termini labeling assisted peptide de novo sequencing.

Cites (10)

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