Protein identification using top-down |
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Authors: | Liu Xiaowen Sirotkin Yakov Shen Yufeng Anderson Gordon Tsai Yihsuan S Ting Ying S Goodlett David R Smith Richard D Bafna Vineet Pevzner Pavel A |
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Institution: | Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, San Diego, California 92093, USA. |
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Abstract: | In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set. |
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