Abstract
Protein peptide identification from a tandem mass spectrum (MS/MS) is a challenging task. Previous approaches for peptide identification with database search are time consuming due to huge search space. De novo sequencing approaches which derive a peptide sequence directly from a MS/MS spectrum usually are of high complexities and the accuracies of the approaches highly depend on the quality of the spectra. In this paper, we developed an accurate and efficient algorithm for peptide identification. Our work consisted of the following steps. Firstly, we found a pair of complementary mass peaks that are b-ion and y-ion, respectively. We then used the two mass peaks as two tree nodes and extend the trees such that in the end the nodes of the trees are elements of a b-ion set and a y-ion set, respectively. Secondly, we applied breadth first search to the trees to generate peptide sequence tags. Finally, we designed a weight function to evaluate the reliabilities of the tags and rank the tags. Our experiment on 2620 experimental MS/MS spectra with one PTM showed that our algorithm achieved better accuracy than other approaches with higher efficiency.
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Li, H., Scott, L., Liu, C., Rwebangira, M., Burge, L., Southerland, W. (2011). Rapid and Accurate Generation of Peptide Sequence Tags with a Graph Search Approach. In: Chen, J., Wang, J., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science(), vol 6674. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21260-4_25
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DOI: https://doi.org/10.1007/978-3-642-21260-4_25
Publisher Name: Springer, Berlin, Heidelberg
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