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LysNDeNovo : An algorithm enabling de novo sequencing of Lys‐N generated peptides fragmented by electron transfer dissociation
Author(s) -
van Breukelen Bas,
Georgiou Alexandros,
Drugan Madalina M.,
Taouatas Nadia,
Mohammed Shabaz,
Heck Albert J. R.
Publication year - 2010
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200900405
Subject(s) - electron transfer dissociation , computational biology , proteomics , chemistry , heuristics , peptide , electron transfer , dissociation (chemistry) , fragmentation (computing) , computer science , algorithm , biology , biochemistry , gene , operating system , organic chemistry
Recently, we introduced a novel proteomics method employing a metalloendopeptidase with Lys‐N specificity to produce proteolytic peptides. Fragmentation spectra generated by electron transfer dissociation, for a large proportion of the Lys‐N proteolytic peptides, were found to be dominated by extensive series of c‐type ions. Taking advantage of this unique spectral property, we developed an algorithm, LysNDeNovo , to facilitate de novo sequencing of these peptides. LysNDeNovo contains simple and naive heuristics to demonstrate a proof of concept, i.e . that Lys‐N peptide electron transfer dissociation spectra are perfectly suited for de novo interpretation. A stringent “golden” dataset of peptides identified by conventional database search algorithms was taken to validate the performance of LysNDeNovo . The results on this dataset indicate that LysNDeNovo was able to confidently identify a considerable proportion (42%), without requiring any prior genome or protein sequences. Results of similar quantity and quality could also be obtained on a much more extensive experimental dataset, illustrating the potential for higher throughput de novo sequencing using these methods.