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

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. 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 4 Da, 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.