期刊
JOURNAL OF PROTEOME RESEARCH
卷 17, 期 5, 页码 1844-1851出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.7b00873
关键词
G-PTM-D; post-translational modification discovery; proteomics; database search; calibration; coisolation; post-translational modification
资金
- National Science Foundation [DBI-1458524]
Correct identification of protein post-translational modifications (PTMs) is crucial to understanding many aspects of protein function in biological processes. G-PTM-D is a recently developed technique for global identification and localization of PTMs. Spectral file calibration prior to applying G-PTM-D, and algorithmic enhancements in the peptide database search significantly increase the accuracy, speed, and scope of PTM identification. We enhance G-PTM-D by using multinotch searches and demonstrate its effectiveness in identification of numerous types of PTMs including high-mass modifications such as glycosylations. The changes described in this work lead to a 20% increase in the number of identified modifications and an order of magnitude decrease in search time. The complete workflow is implemented in MetaMorpheus, a software tool that integrates the database search procedure, identification of coisolated peptides, spectral calibration, and the enhanced GPTM-D workflow. Multinotch searches are also shown to be useful in contexts other than G-PTM-D by producing superior results when used instead of standard narrow-window and open database searches.
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