A spectrum graph-based protein sequence filtering algorithm for proteoform identification by top-down mass spectrometry

Runmin Yang, Daming Zhu, Qiang Kou, Poornima Bhat-Nakshatri, Harikrishna Nakshatri, Si Wu, Xiaowen Liu
2017 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
Database search is the main approach for identifying proteoforms using top-down tandem mass spectra. However, it is extremely slow to align a query spectrum against all protein sequences in a large database when the target proteoform that produced the spectrum contains post-translational modifications and/or mutations. As a result, efficient and sensitive protein sequence filtering algorithms are essential for speeding up database search. In this paper, we propose a novel filtering algorithm,
more » ... ich generates spectrum graphs from subspectra of the query spectrum and searches them against the protein database to find good candidates. Compared with the sequence tag and gaped tag approaches, the proposed method circumvents the step of tag extraction, thus simplifying data processing. Experimental results on real data showed that the proposed method achieved both high speed and high sensitivity in protein sequence filtration.
doi:10.1109/bibm.2017.8217653 pmid:29503761 pmcid:PMC5831147 dblp:conf/bibm/YangZKBNWL17 fatcat:466oebiyybay3cenu577qscwtm