Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder

A SH2-domain-derived superbinder that exhibits strong affinity for phosphotyrosine (pTyr) was used in conjugation with mass spectroscopy approaches to enrich and enable identification of pTyr sites in different cancer cell lines. We present a new strategy for systematic identification of phosphotyro...

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Published inNature chemical biology Vol. 12; no. 11; pp. 959 - 966
Main Authors Bian, Yangyang, Li, Lei, Dong, Mingming, Liu, Xuguang, Kaneko, Tomonori, Cheng, Kai, Liu, Huadong, Voss, Courtney, Cao, Xuan, Wang, Yan, Litchfield, David, Ye, Mingliang, Li, Shawn S-C, Zou, Hanfa
Format Journal Article Book Review
LanguageEnglish
Published New York Nature Publishing Group US 01.11.2016
Nature Publishing Group
Subjects
631/1647/296
631/553
631/92/275
631/92/475
631/92/611
82/1
82/58
Biochemical Engineering
Biochemistry
Bioorganic Chemistry
Cell Biology
Cell Line, Tumor
Chemistry
Chemistry/Food Science
Humans
Kinases
Mass Spectrometry
Peptides
Phosphorylation
Phosphotyrosine - chemistry
Phosphotyrosine - metabolism
Protein Tyrosine Phosphatases - metabolism
Protein-Tyrosine Kinases - metabolism
Proteomics
src Homology Domains
Online AccessGet full text
ISSN1552-4450
1552-4469
1552-4469
DOI10.1038/nchembio.2178

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Abstract A SH2-domain-derived superbinder that exhibits strong affinity for phosphotyrosine (pTyr) was used in conjugation with mass spectroscopy approaches to enrich and enable identification of pTyr sites in different cancer cell lines. We present a new strategy for systematic identification of phosphotyrosine (pTyr) by affinity purification mass spectrometry (AP-MS) using a Src homology 2 (SH2)-domain-derived pTyr superbinder as the affinity reagent. The superbinder allows for markedly deeper coverage of the Tyr phosphoproteome than anti-pTyr antibodies when an optimal amount is used. We identified ∼20,000 distinct phosphotyrosyl peptides and >10,000 pTyr sites, of which 36% were 'novel', from nine human cell lines using the superbinder approach. Tyrosine kinases, SH2 domains and phosphotyrosine phosphatases were preferably phosphorylated, suggesting that the toolkit of kinase signaling is subject to intensive regulation by phosphorylation. Cell-type-specific global kinase activation patterns inferred from label-free quantitation of Tyr phosphorylation guided the design of experiments to inhibit cancer cell proliferation by blocking the highly activated tyrosine kinases. Therefore, the superbinder is a highly efficient and cost-effective alternative to conventional antibodies for systematic and quantitative characterization of the tyrosine phosphoproteome under normal or pathological conditions.
AbstractList We present a new strategy for systematic identification of phosphotyrosine (pTyr) by affinity purification mass spectrometry (AP-MS) using a Src homology 2 (SH2)-domain-derived pTyr superbinder as the affinity reagent. The superbinder allows for markedly deeper coverage of the Tyr phosphoproteome than anti-pTyr antibodies when an optimal amount is used. We identified ~20,000 distinct phosphotyrosyl peptides and >10,000 pTyr sites, of which 36% were 'novel', from nine human cell lines using the superbinder approach. Tyrosine kinases, SH2 domains and phosphotyrosine phosphatases were preferably phosphorylated, suggesting that the toolkit of kinase signaling is subject to intensive regulation by phosphorylation. Cell-type-specific global kinase activation patterns inferred from label-free quantitation of Tyr phosphorylation guided the design of experiments to inhibit cancer cell proliferation by blocking the highly activated tyrosine kinases. Therefore, the superbinder is a highly efficient and cost-effective alternative to conventional antibodies for systematic and quantitative characterization of the tyrosine phosphoproteome under normal or pathological conditions.
We present a new strategy for systematic identification of phosphotyrosine (pTyr) by affinity purification mass spectrometry (AP-MS) using a Src homology 2 (SH2)-domain-derived pTyr superbinder as the affinity reagent. The superbinder allows for markedly deeper coverage of the Tyr phosphoproteome than anti-pTyr antibodies when an optimal amount is used. We identified ∼20,000 distinct phosphotyrosyl peptides and >10,000 pTyr sites, of which 36% were 'novel', from nine human cell lines using the superbinder approach. Tyrosine kinases, SH2 domains and phosphotyrosine phosphatases were preferably phosphorylated, suggesting that the toolkit of kinase signaling is subject to intensive regulation by phosphorylation. Cell-type-specific global kinase activation patterns inferred from label-free quantitation of Tyr phosphorylation guided the design of experiments to inhibit cancer cell proliferation by blocking the highly activated tyrosine kinases. Therefore, the superbinder is a highly efficient and cost-effective alternative to conventional antibodies for systematic and quantitative characterization of the tyrosine phosphoproteome under normal or pathological conditions.We present a new strategy for systematic identification of phosphotyrosine (pTyr) by affinity purification mass spectrometry (AP-MS) using a Src homology 2 (SH2)-domain-derived pTyr superbinder as the affinity reagent. The superbinder allows for markedly deeper coverage of the Tyr phosphoproteome than anti-pTyr antibodies when an optimal amount is used. We identified ∼20,000 distinct phosphotyrosyl peptides and >10,000 pTyr sites, of which 36% were 'novel', from nine human cell lines using the superbinder approach. Tyrosine kinases, SH2 domains and phosphotyrosine phosphatases were preferably phosphorylated, suggesting that the toolkit of kinase signaling is subject to intensive regulation by phosphorylation. Cell-type-specific global kinase activation patterns inferred from label-free quantitation of Tyr phosphorylation guided the design of experiments to inhibit cancer cell proliferation by blocking the highly activated tyrosine kinases. Therefore, the superbinder is a highly efficient and cost-effective alternative to conventional antibodies for systematic and quantitative characterization of the tyrosine phosphoproteome under normal or pathological conditions.
A SH2-domain-derived superbinder that exhibits strong affinity for phosphotyrosine (pTyr) was used in conjugation with mass spectroscopy approaches to enrich and enable identification of pTyr sites in different cancer cell lines. We present a new strategy for systematic identification of phosphotyrosine (pTyr) by affinity purification mass spectrometry (AP-MS) using a Src homology 2 (SH2)-domain-derived pTyr superbinder as the affinity reagent. The superbinder allows for markedly deeper coverage of the Tyr phosphoproteome than anti-pTyr antibodies when an optimal amount is used. We identified ∼20,000 distinct phosphotyrosyl peptides and >10,000 pTyr sites, of which 36% were 'novel', from nine human cell lines using the superbinder approach. Tyrosine kinases, SH2 domains and phosphotyrosine phosphatases were preferably phosphorylated, suggesting that the toolkit of kinase signaling is subject to intensive regulation by phosphorylation. Cell-type-specific global kinase activation patterns inferred from label-free quantitation of Tyr phosphorylation guided the design of experiments to inhibit cancer cell proliferation by blocking the highly activated tyrosine kinases. Therefore, the superbinder is a highly efficient and cost-effective alternative to conventional antibodies for systematic and quantitative characterization of the tyrosine phosphoproteome under normal or pathological conditions.
We present a new strategy for systematic identification of phosphotyrosine (pTyr) by affinity purification mass spectrometry (AP-MS) using a Src homology 2 (SH2)-domain-derived pTyr superbinder as the affinity reagent. The superbinder allows for markedly deeper coverage of the Tyr phosphoproteome than anti-pTyr antibodies when an optimal amount is used. We identified ∼20,000 distinct phosphotyrosyl peptides and >10,000 pTyr sites, of which 36% were 'novel', from nine human cell lines using the superbinder approach. Tyrosine kinases, SH2 domains and phosphotyrosine phosphatases were preferably phosphorylated, suggesting that the toolkit of kinase signaling is subject to intensive regulation by phosphorylation. Cell-type-specific global kinase activation patterns inferred from label-free quantitation of Tyr phosphorylation guided the design of experiments to inhibit cancer cell proliferation by blocking the highly activated tyrosine kinases. Therefore, the superbinder is a highly efficient and cost-effective alternative to conventional antibodies for systematic and quantitative characterization of the tyrosine phosphoproteome under normal or pathological conditions.
Author Kaneko, Tomonori
Bian, Yangyang
Zou, Hanfa
Litchfield, David
Voss, Courtney
Ye, Mingliang
Cheng, Kai
Wang, Yan
Li, Shawn S-C
Liu, Xuguang
Li, Lei
Liu, Huadong
Dong, Mingming
Cao, Xuan
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  organization: Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada., School of Basic Medical Sciences, Qingdao University
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  surname: Dong
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  orcidid: 0000-0002-6045-0244
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  organization: Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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  surname: Litchfield
  fullname: Litchfield, David
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  givenname: Mingliang
  surname: Ye
  fullname: Ye, Mingliang
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  surname: Li
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  email: sli@uwo.ca
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  email: hanfazou@dicp.ac.cn
  organization: Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS)
BackLink https://www.ncbi.nlm.nih.gov/pubmed/27642862$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Book Review
Copyright Springer Nature America, Inc. 2016
Copyright Nature Publishing Group Nov 2016
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Snippet A SH2-domain-derived superbinder that exhibits strong affinity for phosphotyrosine (pTyr) was used in conjugation with mass spectroscopy approaches to enrich...
We present a new strategy for systematic identification of phosphotyrosine (pTyr) by affinity purification mass spectrometry (AP-MS) using a Src homology 2...
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StartPage 959
SubjectTerms 631/1647/296
631/553
631/92/275
631/92/475
631/92/611
82/1
82/58
Biochemical Engineering
Biochemistry
Bioorganic Chemistry
Cell Biology
Cell Line, Tumor
Chemistry
Chemistry/Food Science
Humans
Kinases
Mass Spectrometry
Peptides
Phosphorylation
Phosphotyrosine - chemistry
Phosphotyrosine - metabolism
Protein Tyrosine Phosphatases - metabolism
Protein-Tyrosine Kinases - metabolism
Proteomics
src Homology Domains
Title Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder
URI https://link.springer.com/article/10.1038/nchembio.2178
https://www.ncbi.nlm.nih.gov/pubmed/27642862
https://www.proquest.com/docview/1833935067
https://www.proquest.com/docview/1835376552
https://www.proquest.com/docview/1837318371
Volume 12
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