Motif-centric phosphoproteomics to target kinase-mediated signaling pathways

Tsai, Chia-Feng; Ogata, Kosuke; Sugiyama, Naoyuki; Ishihama, Yasushi

doi:10.1016/j.crmeth.2021.100138

Title: Motif-centric phosphoproteomics to target kinase-mediated signaling pathways

Journal Article · 14 January 2022 · Cell Reports. Methods

DOI: https://doi.org/10.1016/j.crmeth.2021.100138 · OSTI ID:1915278

Tsai, Chia-Feng ^[1]; Ogata, Kosuke ^[2]; Sugiyama, Naoyuki ^[2]; Ishihama, Yasushi ^[3]

Kyoto Univ. (Japan); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Kyoto Univ. (Japan)
Kyoto Univ. (Japan); , National Institute of Biomedical Innovation, Health and Nutrition (Japan)

Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: Japan Science and Technology Agency; Japan Society for the Promotion of Science (JSPS); USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1915278

Report Number(s):: PNNL-SA-169727

Journal Information:: Cell Reports. Methods, Journal Name: Cell Reports. Methods Journal Issue: 1 Vol. 2; ISSN 2667-2375

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (60)

Lowering Sample Requirements to Study Tyrosine Kinase Signaling Using Phosphoproteomics with the TMT Calibrator Approach Fang, Bin; Izumi, Victoria; Rix, Lily L. Remsing PROTEOMICS, Vol. 20, Issue 24 https://doi.org/10.1002/pmic.202000116	journal	September 2020
Casein kinase II phosphorylates p34cdc2 kinase in G1 phase of the HeLa cell division cycle. Russo, G. L.; Vandenberg, M. T.; Yu, I. J. Journal of Biological Chemistry, Vol. 267, Issue 28 https://doi.org/10.1016/S0021-9258(19)88704-5	journal	October 1992
Demonstration of the phosphorylation of dihydropyridine-sensitive calcium channels in chick skeletal muscle and the resultant activation of the channels after reconstitution Mundiña-Weilenmann, C.; Chang, C. F.; Gutierrez, L. M. Journal of Biological Chemistry, Vol. 266, Issue 7 https://doi.org/10.1016/S0021-9258(20)64286-7	journal	March 1991
Signaling—2000 and Beyond Hunter, Tony Cell, Vol. 100, Issue 1 https://doi.org/10.1016/S0092-8674(00)81688-8	journal	January 2000
Tyrosine phosphorylation: thirty years and counting Hunter, Tony Current Opinion in Cell Biology, Vol. 21, Issue 2 https://doi.org/10.1016/j.ceb.2009.01.028	journal	April 2009
Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling Sharma, Kirti; D’Souza, Rochelle C. J.; Tyanova, Stefka Cell Reports, Vol. 8, Issue 5 https://doi.org/10.1016/j.celrep.2014.07.036	journal	September 2014
Quantitative Consequences of Protein Carriers in Immunopeptidomics and Tyrosine Phosphorylation MS2 Analyses Stopfer, Lauren E.; Conage-Pough, Jason E.; White, Forest M. Molecular & Cellular Proteomics, Vol. 20 https://doi.org/10.1016/j.mcpro.2021.100104	journal	January 2021
Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS Thompson, Andrew; Schäfer, Jürgen; Kuhn, Karsten Analytical Chemistry, Vol. 75, Issue 8 https://doi.org/10.1021/ac0262560	journal	April 2003
One-Dimensional Capillary Liquid Chromatographic Separation Coupled with Tandem Mass Spectrometry Unveils the Escherichia coli Proteome on a Microarray Scale Iwasaki, Mio; Miwa, Shohei; Ikegami, Tohru Analytical Chemistry, Vol. 82, Issue 7 https://doi.org/10.1021/ac100343q	journal	March 2010
Sequential Phosphoproteomic Enrichment through Complementary Metal-Directed Immobilized Metal Ion Affinity Chromatography Tsai, Chia-Feng; Hsu, Chuan-Chih; Hung, Jo-Nan Analytical Chemistry, Vol. 86, Issue 1 https://doi.org/10.1021/ac4031175	journal	December 2013
MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes McAlister, Graeme C.; Nusinow, David P.; Jedrychowski, Mark P. Analytical Chemistry, Vol. 86, Issue 14 https://doi.org/10.1021/ac502040v	journal	July 2014
Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-Based Quantitation in Proteomic LC/MS/MS Ogata, Kosuke; Ishihama, Yasushi Analytical Chemistry, Vol. 92, Issue 12 https://doi.org/10.1021/acs.analchem.0c01695	journal	May 2020
Quantifying Kinase-Specific Phosphorylation Stoichiometry Using Stable Isotope Labeling In a Reverse In-Gel Kinase Assay Li, Xiang; Cox, Jonathan T.; Huang, Weiliang Analytical Chemistry, Vol. 88, Issue 23 https://doi.org/10.1021/acs.analchem.6b02599	journal	November 2016
Sensitive, Robust, and Cost-Effective Approach for Tyrosine Phosphoproteome Analysis Dong, Mingming; Bian, Yangyang; Wang, Yan Analytical Chemistry, Vol. 89, Issue 17 https://doi.org/10.1021/acs.analchem.7b02078	journal	August 2017
Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer Hebert, Alexander S.; Prasad, Satendra; Belford, Michael W. Analytical Chemistry, Vol. 90, Issue 15 https://doi.org/10.1021/acs.analchem.8b02233	journal	July 2018
Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells Yi, Lian; Tsai, Chia-Feng; Dirice, Ercument Analytical Chemistry, Vol. 91, Issue 9 https://doi.org/10.1021/acs.analchem.9b00024	journal	March 2019
High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform Dou, Maowei; Clair, Geremy; Tsai, Chia-Feng Analytical Chemistry, Vol. 91, Issue 20 https://doi.org/10.1021/acs.analchem.9b03349	journal	September 2019
Nanoscale Solid-Phase Isobaric Labeling for Multiplexed Quantitative Phosphoproteomics Ogata, Kosuke; Tsai, Chia-Feng; Ishihama, Yasushi Journal of Proteome Research, Vol. 20, Issue 8 https://doi.org/10.1021/acs.jproteome.1c00444	journal	July 2021
Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters Abe, Yuichi; Nagano, Maiko; Tada, Asa Journal of Proteome Research, Vol. 16, Issue 2 https://doi.org/10.1021/acs.jproteome.6b00576	journal	December 2016
Multiplexed Phosphoproteomic Profiling Using Titanium Dioxide and Immunoaffinity Enrichments Reveals Complementary Phosphorylation Events Possemato, Anthony P.; Paulo, Joao A.; Mulhern, Daniel Journal of Proteome Research, Vol. 16, Issue 4 https://doi.org/10.1021/acs.jproteome.6b00905	journal	February 2017
Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring Imamura, Haruna; Wagih, Omar; Niinae, Tomoya Journal of Proteome Research, Vol. 16, Issue 4 https://doi.org/10.1021/acs.jproteome.7b00087	journal	March 2017
Evaluating the Characteristics of Reporter Ion Signal Acquired in the Orbitrap Analyzer for Isobaric Mass Tag Proteome Quantification Experiments Hughes, Christopher S.; Zhu, Chenchen; Spicer, Victor Journal of Proteome Research, Vol. 16, Issue 5 https://doi.org/10.1021/acs.jproteome.7b00092	journal	April 2017
Active Instrument Engagement Combined with a Real-Time Database Search for Improved Performance of Sample Multiplexing Workflows Erickson, Brian K.; Mintseris, Julian; Schweppe, Devin K. Journal of Proteome Research, Vol. 18, Issue 3 https://doi.org/10.1021/acs.jproteome.8b00899	journal	January 2019
Large-Scale Identification of Phosphorylation Sites for Profiling Protein Kinase Selectivity Imamura, Haruna; Sugiyama, Naoyuki; Wakabayashi, Masaki Journal of Proteome Research, Vol. 13, Issue 7 https://doi.org/10.1021/pr500319y	journal	June 2014
Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis Masuda, Takeshi; Tomita, Masaru; Ishihama, Yasushi Journal of Proteome Research, Vol. 7, Issue 2 https://doi.org/10.1021/pr700658q	journal	February 2008
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Cox, Jürgen; Mann, Matthias Nature Biotechnology, Vol. 26, Issue 12 https://doi.org/10.1038/nbt.1511	journal	November 2008
High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics Humphrey, Sean J.; Azimifar, S. Babak; Mann, Matthias Nature Biotechnology, Vol. 33, Issue 9 https://doi.org/10.1038/nbt.3327	journal	August 2015
The origins of protein phosphorylation Cohen, Philip Nature Cell Biology, Vol. 4, Issue 5 https://doi.org/10.1038/ncb0502-e127	journal	May 2002
Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder Bian, Yangyang; Li, Lei; Dong, Mingming Nature Chemical Biology, Vol. 12, Issue 11 https://doi.org/10.1038/nchembio.2178	journal	September 2016
Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics Tsai, Chia-Feng; Wang, Yi-Ting; Yen, Hsin-Yung Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms7622	journal	March 2015
pLogo: a probabilistic approach to visualizing sequence motifs O'Shea, Joseph P.; Chou, Michael F.; Quader, Saad A. Nature Methods, Vol. 10, Issue 12 https://doi.org/10.1038/nmeth.2646	journal	October 2013
The Perseus computational platform for comprehensive analysis of (prote)omics data Tyanova, Stefka; Temu, Tikira; Sinitcyn, Pavel Nature Methods, Vol. 13, Issue 9 https://doi.org/10.1038/nmeth.3901	journal	June 2016
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips Rappsilber, Juri; Mann, Matthias; Ishihama, Yasushi Nature Protocols, Vol. 2, Issue 8 https://doi.org/10.1038/nprot.2007.261	journal	August 2007
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Huang, Da Wei; Sherman, Brad T.; Lempicki, Richard A. Nature Protocols, Vol. 4, Issue 1 https://doi.org/10.1038/nprot.2008.211	journal	December 2008
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics Tyanova, Stefka; Temu, Tikira; Cox, Juergen Nature Protocols, Vol. 11, Issue 12 https://doi.org/10.1038/nprot.2016.136	journal	October 2016
Multiple levels of cyclin specificity in cell-cycle control Bloom, Joanna; Cross, Frederick R. Nature Reviews Molecular Cell Biology, Vol. 8, Issue 2 https://doi.org/10.1038/nrm2105	journal	February 2007
Benchmarking common quantification strategies for large-scale phosphoproteomics Hogrebe, Alexander; von Stechow, Louise; Bekker-Jensen, Dorte B. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03309-6	journal	March 2018
Defining the carrier proteome limit for single-cell proteomics Cheung, Tommy K.; Lee, Chien-Yun; Bayer, Florian P. Nature Methods, Vol. 18, Issue 1 https://doi.org/10.1038/s41592-020-01002-5	journal	December 2020
Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry Mertins, Philipp; Tang, Lauren C.; Krug, Karsten Nature Protocols, Vol. 13, Issue 7 https://doi.org/10.1038/s41596-018-0006-9	journal	July 2018
Large-scale Discovery of Substrates of the Human Kinome Sugiyama, Naoyuki; Imamura, Haruna; Ishihama, Yasushi Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-46385-4	journal	July 2019
Phosphoproteomics Reveals HMGA1, a CK2 Substrate, as a Drug-Resistant Target in Non-Small Cell Lung Cancer Wang, Yi-Ting; Pan, Szu-Hua; Tsai, Chia-Feng Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep44021	journal	March 2017
Large-scale phosphorylation analysis of mouse liver Villen, J.; Beausoleil, S. A.; Gerber, S. A. Proceedings of the National Academy of Sciences, Vol. 104, Issue 5 https://doi.org/10.1073/pnas.0609836104	journal	January 2007
Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates Xue, L.; Wang, W. -H.; Iliuk, A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 15 https://doi.org/10.1073/pnas.1119418109	journal	March 2012
Transforming gene product of Rous sarcoma virus phosphorylates tyrosine Hunter, Tony; Sefton, Bartholomew M. Proceedings of the National Academy of Sciences, Vol. 77, Issue 3 https://doi.org/10.1073/pnas.77.3.1311	journal	March 1980
PTMScan Direct: Identification and Quantification of Peptides from Critical Signaling Proteins by Immunoaffinity Enrichment Coupled with LC-MS/MS Stokes, Matthew P.; Farnsworth, Charles L.; Moritz, Albrecht Molecular & Cellular Proteomics, Vol. 11, Issue 5 https://doi.org/10.1074/mcp.M111.015883	journal	May 2012
Identification of Direct Tyrosine Kinase Substrates Based on Protein Kinase Assay-Linked Phosphoproteomics Xue, Liang; Geahlen, Robert L.; Tao, W. Andy Molecular & Cellular Proteomics, Vol. 12, Issue 10 https://doi.org/10.1074/mcp.O113.027722	journal	October 2013
Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM) Gallien, Sebastien; Kim, Sang Yoon; Domon, Bruno Molecular & Cellular Proteomics, Vol. 14, Issue 6 https://doi.org/10.1074/mcp.O114.043968	journal	March 2015
An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics Tsai, Chia-Feng; Zhao, Rui; Williams, Sarah M. Molecular & Cellular Proteomics, Vol. 19, Issue 5 https://doi.org/10.1074/mcp.RA119.001857	journal	May 2020
Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome Chua, Xien Yu; Mensah, Theresa; Aballo, Timothy Molecular & Cellular Proteomics, Vol. 19, Issue 4 https://doi.org/10.1074/mcp.TIR119.001865	journal	April 2020
A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients Bekker-Jensen, Dorte B.; Martínez-Val, Ana; Steigerwald, Sophia Molecular & Cellular Proteomics, Vol. 19, Issue 4 https://doi.org/10.1074/mcp.TIR119.001906	journal	February 2020
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations Hornbeck, Peter V.; Zhang, Bin; Murray, Beth Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1267	journal	December 2014
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Szklarczyk, Damian; Gable, Annika L.; Lyon, David Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1131	journal	November 2018
The jPOST environment: an integrated proteomics data repository and database Moriya, Yuki; Kawano, Shin; Okuda, Shujiro Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky899	journal	October 2018
Illuminating the dark phosphoproteome Needham, Elise J.; Parker, Benjamin L.; Burykin, Timur Science Signaling, Vol. 12, Issue 565 https://doi.org/10.1126/scisignal.aau8645	journal	January 2019
A structural basis for substrate specificities of protein Ser/Thr kinases: primary sequence preference of casein kinases I and II, NIMA, phosphorylase kinase, calmodulin-dependent kinase II, CDK5, and Erk1. Songyang, Z.; Lu, K. P.; Kwon, Y. T. Molecular and Cellular Biology, Vol. 16, Issue 11 https://doi.org/10.1128/MCB.16.11.6486	journal	November 1996
High-Density, Targeted Monitoring of Tyrosine Phosphorylation Reveals Activated Signaling Networks in Human Tumors Stopfer, Lauren E.; Flower, Cameron T.; Gajadhar, Aaron S. Cancer Research, Vol. 81, Issue 9 https://doi.org/10.1158/0008-5472.CAN-20-3804	journal	January 2021
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation Budnik, Bogdan; Levy, Ezra; Harmange, Guillaume Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1547-5	journal	October 2018
The casein kinase 2 inhibitor, CX-4945, as an anti-cancer drug in treatment of human hematological malignancies Chon, Hae J.; Bae, Kyoung J.; Lee, Yura Frontiers in Pharmacology, Vol. 6 https://doi.org/10.3389/fphar.2015.00070	journal	March 2015
Complementary PTM Profiling of Drug Response in Human Gastric Carcinoma by Immunoaffinity and IMAC Methods with Total Proteome Analysis Stokes, Matthew; Farnsworth, Charles; Gu, Hongbo Proteomes, Vol. 3, Issue 3 https://doi.org/10.3390/proteomes3030160	journal	August 2015
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation Budnik, Bogdan; Levy, Ezra; Harmange, Guillaume Figshare https://doi.org/10.6084/m9.figshare.c.4274000.v1	collection	January 2018

Similar Records

An integrative analysis of tumor proteomic and phosphoproteomic profiles to examine the relationships between kinase activity and phosphorylation

Journal Article · 2019 · Molecular and Cellular Proteomics · OSTI ID:1572488

Arshad, Osama A.; Danna, Vincent G.; Petyuk, Vladislav A.; +4 more

Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹⁸O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography

Journal Article · 2008 · Journal of Proteome Research, 7(10):4215-24 · OSTI ID:974991

Ding, Shi-Jian; Wang, Yingchun; Jacobs, Jon M; +14 more

Quantitative cardiac phosphoproteomics profiling during ischemia-reperfusion in an immature swine model

Journal Article · 2017 · American Journal of Physiology: Heart and Circulatory Physiology · OSTI ID:1378020

Ledee, Dolena R.; Kang, Min A.; Kajimoto, Masaki; +4 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
EGFR signaling network
TMT quantitation
boosting MS signal
in vitro kinase reaction
isobaric tag
kinase-substrate relationship
motif-centric
phosphopeptide enrichment
phosphoproteome
tyrosine phosphoproteome

Title: Motif-centric phosphoproteomics to target kinase-mediated signaling pathways

Citation Formats

References (60)

Similar Records

Related Subjects