Journal
JOURNAL OF PROTEOME RESEARCH
Volume 16, Issue 2, Pages 645-654Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.6b00716
Keywords
tandem mass spectrometry; de novo peptide sequencing; dynamic programming; unexpected modifications
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Funding
- National Key Research and Development Program of China [2016YFA0501301]
- National High Technology Research and Development Program of China (863) [2014AA020902, 2014AA020901]
- National Natural Science Foundation of China [31470805]
- Youth Innovation Promotion Association CAS [2014091]
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De novo peptide sequencing has improved remarkably, but sequencing full-length peptides with unexpected modifications is still a challenging problem. Here we present an open de novo sequencing tool, Open-pNovo, for de novo sequencing of peptides with arbitrary types of modifications. Although the search space increases by 300 times, Open-pNovo is close to or even similar to 10-times faster than the other three proposed algorithms. Furthermore, considering top-1 candidates on three MS/MS data sets, Open-pNovo can recall over 90% of the results obtained by any one traditional algorithm and report 5-87% more peptides, including 14-250% more modified peptides. On a high-quality simulated data set, similar to 85% peptides with arbitrary modifications can be recalled by Open-pNovo, while hardly any results can be recalled by others. In summary, Open-pNovo is an excellent tool for open de novo sequencing and has great potential for discovering unexpected modifications in the real biological applications.
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