Journal
JOURNAL OF PROTEOME RESEARCH
Volume 13, Issue 10, Pages 4470-4478Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr5008015
Keywords
histone; proteomics; post-translational modification; data analysis; search engine
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Funding
- NIH from the Office of the Director [DP2OD007447]
- National Science Foundation (NSF) Early Faculty CAREER award
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [1262672] Funding Source: National Science Foundation
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Identification of histone post-translational modifications (PTMs) is challenging for proteomics search engines. Including many histone PTMs in one search increases the number of candidate peptides dramatically, leading to low search speed and fewer identified spectra. To evaluate database search engines on identifying histone PTMs, we present a method in which one kind of modification is searched each time, for example, unmodified, individually modified, and multimodified, each search result is filtered with false discovery rate less than 1%, and the identifications of multiple search engines are combined to obtain confident results. We apply this method for eight search engines on histone data sets. We find that two search engines, pFind and Mascot, identify most of the confident results at a reasonable speed, so we recommend using them to identify histone modifications. During the evaluation, we also find some important aspects for the analysis of histone modifications. Our evaluation of different search engines on identifying histone modifications will hopefully help those who are hoping to enter the histone proteomics field. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD001118.
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