Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics

Chia-Feng Tsai, Yi-Ting Wang, Hsin-Yung Yen, Chih-Chiang Tsou, Wei-Chi Ku, Pei-Yi Lin, Hsuan-Yu Chen, Alexey I. Nesvizhskii, Yasushi Ishihama () and Yu-Ju Chen ()
Additional contact information
Chia-Feng Tsai: National Taiwan University
Yi-Ting Wang: Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
Hsin-Yung Yen: Institute of Biochemical Sciences, National Taiwan University
Chih-Chiang Tsou: University of Michigan Medical School
Wei-Chi Ku: School of Medicine, Fu Jen Catholic University
Pei-Yi Lin: Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
Hsuan-Yu Chen: Institute of Statistical Science, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
Alexey I. Nesvizhskii: University of Michigan Medical School
Yasushi Ishihama: Graduate School of Pharmaceutical Sciences, Kyoto University
Yu-Ju Chen: National Taiwan University

Nature Communications, 2015, vol. 6, issue 1, 1-8

Abstract: Abstract Our ability to model the dynamics of signal transduction networks will depend on accurate methods to quantify levels of protein phosphorylation on a global scale. Here we describe a motif-targeting quantitation method for phosphorylation stoichiometry typing. Proteome-wide phosphorylation stoichiometry can be obtained by a simple phosphoproteomic workflow integrating dephosphorylation and isotope tagging with enzymatic kinase reaction. Proof-of-concept experiments using CK2-, MAPK- and EGFR-targeting assays in lung cancer cells demonstrate the advantage of kinase-targeted complexity reduction, resulting in deeper phosphoproteome quantification. We measure the phosphorylation stoichiometry of >1,000 phosphorylation sites including 366 low-abundance tyrosine phosphorylation sites, with high reproducibility and using small sample sizes. Comparing drug-resistant and sensitive lung cancer cells, we reveal that post-translational phosphorylation changes are significantly more dramatic than those at the protein and messenger RNA levels, and suggest potential drug targets within the kinase–substrate network associated with acquired drug resistance.

Date: 2015
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/ncomms7622 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7622

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms7622

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().