title: Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications.
abstract: 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 ∼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, ∼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.
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Hao
authors.identifier: 0000-0002-1277-2628
authors.initials: H
authors.lastname: Yang
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Chi
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Wen-Jing
authors.initials: WJ
authors.lastname: Zhou
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Wen-Feng
authors.initials: WF
authors.lastname: Zeng
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Kun
authors.initials: K
authors.lastname: He
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Liu
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China.
authors.forename: Rui-Xiang
authors.initials: RX
authors.lastname: Sun
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Si-Min
authors.initials: SM
authors.lastname: He
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics*; D030562:Databases, Protein; D010455:Peptides / Q000235:genetics*; D011499:Protein Processing, Post-Translational / Q000235:genetics*; D020539:Sequence Analysis, Protein; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides
keywords: de novo peptide sequencing; dynamic programming; tandem mass spectrometry; unexpected modifications