Title :
Blind identification of post-translational modifications via dynamic time warping model
Author :
Li, Hui ; Liu, Chunmei ; Southerland, William
Author_Institution :
Dept. of Syst. & Comput. Sci., Howard Univ., Washington, DC, USA
Abstract :
Post-translation modification (PTM) plays a significant role in the understanding of protein functions. However, PTM identification is a very challenging problem in proteomics research field. In this paper, a dynamic time warping (DTW) model is introduced to find the optimal match between an experimental tandem mass spectrum (MS/MS) and a theoretical spectrum generated from a peptide sequence in a peptide database. Our approach can identify all types of PTMs in a blind mode. The test results on experimental spectra that contain no PTM, one PTM and two PTMs show that our approach can identify 95%, 93%, and 34% correct peptide sequences as the top 1 candidates, respectively, which is much better than other blind search methods.
Keywords :
biochemistry; bioinformatics; mass spectroscopy; proteins; proteomics; time warp simulation; blind identification; blind search method; dynamic time warping model; peptide database; peptide sequence; post-translational modification; protein function; proteomics research; tandem mass spectrum; theoretical spectrum; Arrays; Databases; Doped fiber amplifiers; Ions; Noise; Peptides; Proteins; deterministic finite automata; dynamic time warping; post-translational modification; tandem mass spectrum (MS/MS);
Conference_Titel :
Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2012 IEEE Symposium on
Conference_Location :
San Diego, CA
Print_ISBN :
978-1-4673-1190-8
DOI :
10.1109/CIBCB.2012.6217230
