Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-04-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/28/9/3675 |
| _version_ | 1797602151833272320 |
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| author | Andrew G. DeMarco Mark C. Hall |
| author_facet | Andrew G. DeMarco Mark C. Hall |
| author_sort | Andrew G. DeMarco |
| collection | DOAJ |
| description | Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes. |
| first_indexed | 2024-03-11T04:11:57Z |
| format | Article |
| id | doaj.art-2fdf4dcf468245c3af5cca6849db60b4 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-11T04:11:57Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-2fdf4dcf468245c3af5cca6849db60b42023-11-17T23:21:57ZengMDPI AGMolecules1420-30492023-04-01289367510.3390/molecules28093675Phosphoproteomic Approaches for Identifying Phosphatase and Kinase SubstratesAndrew G. DeMarco0Mark C. Hall1Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USADepartment of Biochemistry, Purdue University, West Lafayette, IN 47907, USAProtein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes.https://www.mdpi.com/1420-3049/28/9/3675phosphorylationpost-translation modificationPTMmass spectrometryphosphoproteomicsquantitative proteomics |
| spellingShingle | Andrew G. DeMarco Mark C. Hall Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates Molecules phosphorylation post-translation modification PTM mass spectrometry phosphoproteomics quantitative proteomics |
| title | Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates |
| title_full | Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates |
| title_fullStr | Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates |
| title_full_unstemmed | Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates |
| title_short | Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates |
| title_sort | phosphoproteomic approaches for identifying phosphatase and kinase substrates |
| topic | phosphorylation post-translation modification PTM mass spectrometry phosphoproteomics quantitative proteomics |
| url | https://www.mdpi.com/1420-3049/28/9/3675 |
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