期刊
JOURNAL OF PROTEOME RESEARCH
卷 21, 期 6, 页码 1575-1587出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.2c00198
关键词
phosphoproteomics; kinase enrichment; phosphorite annotations; phosphosites database; mass spectrometry; tandem mass tags; SARS-CoV-2
资金
- German Ministry of Education and Research (BMBF) [031L0220B]
Phosphoproteomics quantifies phosphorylation site changes, but functional analysis is challenging. A new database, iKiP-DB, accurately predicts kinase activity changes and is applied in a SARS-CoV-2 study.
Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, the vast majority of known sites is not assigned to any protein kinase. Assigning changes in the phosphoproteome to the activity of individual kinases therefore remains a key challenge. A recent large-scale study systematically identified in vitro substrates for most human protein kinases. Here, we reprocessed and filtered these data to generate an in vitro Kinase-to-Phosphosite database (iKiP-DB). We show that iKiP-DB can accurately predict changes in kinase activity in published phosphoproteomic data sets for both well-studied and poorly characterized kinases. We apply iKiP-DB to a newly generated phosphoproteomic analysis of SARS-CoV-2 infected human lung epithelial cells and provide evidence for coronavirus-induced changes in host cell kinase activity. In summary, we show that iKiP-DB is widely applicable to facilitate the functional analysis of phosphoproteomic data sets.
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