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Wang Z, Tan J, Li M, Gao C, Li W, Xu J, Guo C, Chen Z, Cai R. Clickable Photoreactive ATP-Affinity Probe for Global Profiling of ATP-Binding Proteins. Anal Chem 2023; 95:17533-17540. [PMID: 37993803 DOI: 10.1021/acs.analchem.3c02694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Adenosine triphosphate (ATP) is the major energy carrier in organisms, and there are many cellular proteins that can bind to ATP. Among these proteins, kinases are key regulators in several cell signaling processes, and aberrant kinase signaling contributes to the development of many human diseases, including cancer. Hence, small-molecule kinase inhibitors have been successfully used for the treatment of various diseases. Since the ATP-binding pockets are similar for many kinases, it is very important to evaluate the selectivity of different kinase inhibitors. We report here a clickable ATP photoaffinity probe for the global profiling of ATP-binding proteins. After incubating the protein lysate with the ATP probe followed by ultraviolet (UV) irradiation, ATP-binding proteins were labeled with an alkyne handle for subsequent biotin conjugation through click chemistry. Labeled proteins were enriched with streptavidin beads, digested with trypsin, and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). More than 400 ATP-binding proteins, including approximately 200 kinases, could be identified in a single LC-MS/MS run in the data-dependent acquisition mode. We then applied this method to the analysis of targets of three selected ATP-competitive kinase inhibitors. We were able to successfully identify some of their reported target proteins from label-free quantification results and validated the results using Western blot analyses. Together, we developed a clickable ATP photoaffinity probe for proteome-wide profiling of ATP-binding proteins and demonstrated that this chemoproteomic method is amenable to high-throughput target identification of kinase inhibitors.
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Affiliation(s)
- Zhiming Wang
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
| | - Jing Tan
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
| | - Mengxuan Li
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Can Gao
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Wenwen Li
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Jing Xu
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Changchuan Guo
- Shandong Institute for Food and Drug Control, Jinan 250101, Shandong, China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, Shandong, China
| | - Rong Cai
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
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2
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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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Zhang Q, Dong X, Lu J, Song J, Wang Y. Chemoproteomic Approach toward Probing the Interactomes of Perfluoroalkyl Substances. Anal Chem 2021; 93:9634-9639. [PMID: 34185510 PMCID: PMC8760635 DOI: 10.1021/acs.analchem.1c01948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Poly- and perfluoroalkyl substances (PFASs) are widely used in industrial products and consumer goods. Due to their extremely recalcitrant nature and potential bioaccumulation and toxicity, exposure to PFASs may result in adverse health outcomes in humans and wildlife. In this study, we developed a chemoproteomic strategy, based on the use of isotope-coded desthiobiotin-perfluorooctanephosphonic acid (PFOPA) probe and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis, to profile PFAS-binding proteins. Targeted proteins were labeled with the desthiobiotin-PFOPA probe, digested with trypsin, and the ensuing desthiobiotin-conjugated peptides were enriched with streptavidin beads for LC-MS/MS analysis. We were able to identify 469 putative PFOPA-binding proteins. By conducting competitive binding experiments using low (10 μM) and high (100 μM) concentrations of stable isotope-labeled PFOPA probes, we further identified 128 nonredundant peptides derived from 75 unique proteins that exhibit selective binding toward PFOPA. Additionally, we demonstrated that one of these proteins, fatty acid-binding protein 5 (FABP5), could interact directly with PFASs, including perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), perfluorohexanesulfonic acid (PFHxS), and perfluorobutanesulfonic acid (PFBS). Furthermore, desthiobiotin-labeled lysine residues are located close to the fatty acid-binding pocket of FABP5, and the binding affinity varies with the structures of PFASs. Taken together, we developed a novel chemoproteomic method for interrogating the PFAS-interacting proteome. The identification of these proteins sets the stage for understanding the mechanisms through which exposure to PFASs confers adverse human health effects.
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Liu Y, Qu M, Pan M, Zheng X, Sheng Y, Ji Y, You C, Dai X. Chemical proteomic profiling of UTP-binding proteins in human cells. Anal Chim Acta 2021; 1168:338607. [PMID: 34052001 DOI: 10.1016/j.aca.2021.338607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/20/2022]
Abstract
Nucleotide-binding proteins play important roles in a variety of biological processes. While ATP- and GTP-binding proteins have been well studied, the systematical identification of UTP-interacting proteins remains under investigated. Here, we developed a chemical proteomic strategy using a biotinylated UTP affinity probe coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) method to enrich, identify and quantify UTP-binding proteins at the entire proteome scale. By performing labeling reactions with high vs low concentrations of UTP probe (100 and 10 μM) or with the UTP probe in the presence of free UTP in stable isotope labeling by amino acids in cell culture (SILAC) experiments, we identified more than 70 potential UTP-binding proteins which are involved in multiple cellular processes, such as translational elongation and protein folding. We also validated the UTP-binding capability of the cytoskeletal protein ACTB by using cellular thermal shift assay (CETSA). Together, we performed a high-throughput chemical proteomics-based analysis to identify, for the first time, UTP-binding proteins in human proteome, which should be applicable for the identification and quantification of UTP-binding proteins in other organisms.
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Affiliation(s)
- Yunming Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Minghui Qu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Mengting Pan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xiaofang Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Yuwei Sheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Yongqin Ji
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Changjun You
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Xiaoxia Dai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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Huang M, Wang Y. GLOBAL AND TARGETED PROFILING OF GTP-BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:215-235. [PMID: 32519381 PMCID: PMC7725852 DOI: 10.1002/mas.21637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/15/2020] [Indexed: 05/05/2023]
Abstract
GTP-binding proteins are among the most important enzyme families that are involved in a plethora of biological processes. However, owing to the enormous diversity of the nucleotide-binding protein family, comprehensive analyses of the expression level, structure, activity, and regulatory mechanisms of GTP-binding proteins remain challenging with the use of conventional approaches. The many advances in mass spectrometry (MS) instrumentation and data acquisition methods, together with a variety of enrichment approaches in sample preparation, render MS a powerful tool for the comprehensive characterizations of the activities and expression levels of various GTP-binding proteins. We review herein the recent developments in the application of MS-based techniques, together with general and widely used affinity enrichment approaches, for the proteome-wide and targeted capture, identification, and quantification of GTP-binding proteins. The working principles, advantages, and limitations of various strategies for profiling the expression level, activity, posttranslational modifications, and interactome of GTP-binding proteins are discussed. It can be envisaged that future applications of MS-based proteomics will lead to a better understanding about the roles of GTP-binding proteins in different biological processes and human diseases. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Ming Huang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
- Correspondence author: Yinsheng Wang. Telephone: (951)827-2700;
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Suraj J, Kurpińska A, Olkowicz M, Niedzielska-Andres E, Smolik M, Zakrzewska A, Jasztal A, Sitek B, Chlopicki S, Walczak M. Development, validation and application of a micro-liquid chromatography-tandem mass spectrometry based method for simultaneous quantification of selected protein biomarkers of endothelial dysfunction in murine plasma. J Pharm Biomed Anal 2017; 149:465-474. [PMID: 29172146 DOI: 10.1016/j.jpba.2017.11.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/31/2017] [Accepted: 11/05/2017] [Indexed: 11/24/2022]
Abstract
The objective of this study was to develop and validate the method based on micro-liquid chromatography-tandem mass spectrometry (microLC/MS-MRM) for simultaneous determination of adiponectin (ADN), von Willebrand factor (vWF), soluble form of vascular cell adhesion molecule 1 (sVCAM-1), soluble form of intercellular adhesion molecule 1 (sICAM-1) and syndecan-1 (SDC-1) in mouse plasma. The calibration range was established from 2.5pmol/mL to 5000pmol/mL for ADN; 5pmol/mL to 5000pmol/mL for vWF; 0.375pmol/mL to 250pmol/mL for sVCAM-1 and sICAM-1; and 0.25pmol/mL to 250pmol/mL for SDC-1. The method was applied to measure the plasma concentration of selected proteins in mice fed high-fat diet (HFD), and revealed the pro-thrombotic status by increased concentration of vWF (1.31±0.17 nmol/mL (Control) vs 1.98±0.09 nmol/mL (HFD), p <0.05) and the dysregulation of adipose tissue metabolism by decreased concentration of ADN (0.62±0.08 nmol/mL (Control) vs 0.37±0.06 nmol/mL (HFD), p <0.05). In conclusion, the microLC/MS-MRM-based method allows for reliable measurements of selected protein biomarkers of endothelial dysfunction in mouse plasma.
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Affiliation(s)
- Joanna Suraj
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics, Bobrzynskiego 14, 30-348, Krakow, Poland; Jagiellonian University Medical College, Faculty of Pharmacy, Chair and Department of Toxicology, Medyczna 9, 30-688, Krakow, Poland
| | - Anna Kurpińska
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Mariola Olkowicz
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Ewa Niedzielska-Andres
- Jagiellonian University Medical College, Faculty of Pharmacy, Chair and Department of Toxicology, Medyczna 9, 30-688, Krakow, Poland
| | - Magdalena Smolik
- Jagiellonian University Medical College, Faculty of Pharmacy, Chair and Department of Toxicology, Medyczna 9, 30-688, Krakow, Poland
| | - Agnieszka Zakrzewska
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Agnieszka Jasztal
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Barbara Sitek
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Stefan Chlopicki
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics, Bobrzynskiego 14, 30-348, Krakow, Poland; Jagiellonian University Medical College, Faculty of Medicine, Chair of Pharmacology, Grzegorzecka 16, 31-531, Krakow, Poland
| | - Maria Walczak
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics, Bobrzynskiego 14, 30-348, Krakow, Poland; Jagiellonian University Medical College, Faculty of Pharmacy, Chair and Department of Toxicology, Medyczna 9, 30-688, Krakow, Poland.
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8
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Li S, Diego-Limpin PA, Bajrami B, Keshipeddy S, Lam YW, Deng B, Farrokhi V, McShane AJ, Nemati R, Howell AR, Yao X. Scaling Proteome-Wide Reactions of Activity-Based Probes. Anal Chem 2017; 89:6295-6299. [PMID: 28570047 DOI: 10.1021/acs.analchem.7b01184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Unified analysis of complex reactions of an activity-based probe with proteins in a proteome remains an unsolved challenge. We propose a power expression, rate = kobs[Probe]α, for scaling the progress of proteome-wide reactions and use the scaling factor (0 ≤ α ≤ 1) as an apparent, partial order with respect to the probe to measure the "enzyme-likeness" for a protein in reaction acceleration. Thus, α reports the intrinsic reactivity of the protein with the probe. When α = 0, the involved protein expedites the reaction to the maximal degree; when α = 1, the protein reacts with the probe via an unaccelerated, bimolecular reaction. The selectivity (β) of the probe reacting with two proteins is calculated as a ratio of conversion factors (kobs values) for corresponding power equations. A combination of α and β provides a tiered system for quantitatively assessing the probe efficacy; an ideal probe exhibits high reactivity with its protein targets (low in α) and is highly selective (high in β) in forming the probe-protein adducts. The scaling analysis was demonstrated using proteome-wide reactions of HT-29 cell lysates with a model probe of threonine β-lactone.
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Affiliation(s)
- Song Li
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Pamela A Diego-Limpin
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Bekim Bajrami
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Santosh Keshipeddy
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Ying-Wai Lam
- Department of Biology, University of Vermont , Burlington, Vermont 05405, United States.,Vermont Genetics Network Proteomics Facility, University of Vermont , Burlington, Vermont 05405, United States
| | - Bin Deng
- Department of Biology, University of Vermont , Burlington, Vermont 05405, United States.,Vermont Genetics Network Proteomics Facility, University of Vermont , Burlington, Vermont 05405, United States
| | - Vahid Farrokhi
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Adam J McShane
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Reza Nemati
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Amy R Howell
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Xudong Yao
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States.,Institute for Systems Biology, University of Connecticut , Storrs, Connecticut 06269, United States
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9
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Miao W, Xiao Y, Guo L, Jiang X, Huang M, Wang Y. A High-Throughput Targeted Proteomic Approach for Comprehensive Profiling of Methylglyoxal-Induced Perturbations of the Human Kinome. Anal Chem 2016; 88:9773-9779. [PMID: 27626823 DOI: 10.1021/acs.analchem.6b02816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are one of the most important families of enzymes that are involved in numerous cell signaling processes. Existing methods for studying kinase expression and activation have limited kinome coverage. Herein we established a multiple-reaction monitoring (MRM)-based targeted proteomic method that provided an unprecedented coverage (∼80%) of the human kinome. We employed this method for profiling comprehensively the alterations of the global kinome of HEK293T human embryonic kidney cells upon treatment with methylglyoxal, a glycolysis byproduct that is present at elevated levels in blood and tissues of diabetic patients and is thought to contribute to diabetic complications. Our results led to the quantification of 328 unique kinases. In particular, we found that methylglyoxal treatment gave rise to altered expression of a number of kinases in the MAPK pathway and diminished expression of several receptor tyrosine kinases, including epidermal growth factor receptor (EGFR), insulin growth factor 2 receptor (IGF2R), fibroblast growth factor receptor (FGFR), etc. Furthermore, we demonstrated that the diminished expression of EGFR occurred through a mechanism that is distinct from the reduced expression of IGF2R and FGFR1. Together, our targeted kinome profiling method offers a powerful resource for exploring kinase-mediated signaling pathways that are altered by extracellular stimuli, and the results from the present study suggest new mechanisms underlying the development of diabetic complications.
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Affiliation(s)
- Weili Miao
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Yongsheng Xiao
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Lei Guo
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Xiaogang Jiang
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Ming Huang
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
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10
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Song Q, Song Y, Zhang N, Li J, Jiang Y, Zhang K, Zhang Q, Tu P. Potential of hyphenated ultra-high performance liquid chromatography-scheduled multiple reaction monitoring algorithm for large-scale quantitative analysis of traditional Chinese medicines. RSC Adv 2015. [DOI: 10.1039/c5ra09429a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The combination of a core–shell ADME column with a sMRM algorithm offers the potential for large-scale quantitative analysis of the components in TCMs by providing not only high quality quantitative signals but also reliable MS2 spectra.
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Affiliation(s)
- Qingqing Song
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
- School of Chinese Materia Medica
| | - Yuelin Song
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Na Zhang
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
- School of Chinese Materia Medica
| | - Jun Li
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Yong Jiang
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing 100191
- China
| | - Kerong Zhang
- Application Support Center
- AB SCIEX
- Shanghai 200233
- China
| | - Qian Zhang
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
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