Protein Identification Using Top-Down

Liu, Xiaowen; Sirotkin, Yakov; Shen, Yufeng; Anderson, Gordon A; Tsai, Yi-Hsuan S; Ting, Ying S; Goodlett, David R; Smith, Richard D; Bafna, Vineet; Pevzner, Pavel A

doi:10.1074/mcp.m111.008524

DOE OSTI · 1052931

Protein Identification Using Top-Down

Liu, Xiaowen·Sirotkin, Yakov·Shen, Yufeng·Anderson, Gordon A·Tsai, Yi-Hsuan S·Ting, Ying S·Goodlett, David R·Smith, Richard D·Bafna, Vineet·Pevzner, Pavel A

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Abstract

In the last two years, due to 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 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 (PTMs). We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark MS-Align+ along with PIITA, ProSightPTM and SEQUEST, which were previously used for top-down MS/MS database searches. We demonstrate that MS-Align+ and PIITA significantly increase the number of identified proteins as compared to ProSightPTM and SEQUEST.

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Liu, Xiaowen, Sirotkin, Yakov, Shen, Yufeng, Anderson, Gordon A, Tsai, Yi-Hsuan S, Ting, Ying S, Goodlett, David R, Smith, Richard D, Bafna, Vineet, Pevzner, Pavel A. 2012-06-01. Protein Identification Using Top-Down. https://doi.org/10.1074/mcp.m111.008524

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