{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T10:59:31Z","timestamp":1788951571171,"version":"build-2803163510"},"reference-count":109,"publisher":"Elsevier BV","issue":"8","license":[{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,6,15]],"date-time":"2024-06-15T00:00:00Z","timestamp":1718409600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012165","name":"Key Technologies Research and Development Program","doi-asserted-by":"publisher","award":["2021YFA1300402"],"award-info":[{"award-number":["2021YFA1300402"]}],"id":[{"id":"10.13039\/501100012165","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020950","name":"National Science and Technology Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020595","name":"National Science and Technology Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020595","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32300261"],"award-info":[{"award-number":["32300261"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["112-2311-B-001-024-MY3"],"award-info":[{"award-number":["112-2311-B-001-024-MY3"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["110-2311-B-001-043-MY2"],"award-info":[{"award-number":["110-2311-B-001-043-MY2"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["mcponline.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular & Cellular Proteomics"],"published-print":{"date-parts":[[2024,8]]},"DOI":"10.1016\/j.mcpro.2024.100804","type":"journal-article","created":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T19:35:09Z","timestamp":1718739309000},"page":"100804","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":22,"title":["DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis"],"prefix":"10.1016","volume":"23","author":[{"given":"Tian","family":"Sang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4415-2925","authenticated-orcid":false,"given":"Chin-Wen","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-4574-6235","authenticated-orcid":false,"given":"Zhen","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanyan","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-1731-5362","authenticated-orcid":false,"given":"Pei-Yi","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4453-5854","authenticated-orcid":false,"given":"Marco","family":"Hadisurya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Kang","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaobo","family":"Lang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5535-5517","authenticated-orcid":false,"given":"W. Andy","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7100-1401","authenticated-orcid":false,"given":"Chuan-Chih","family":"Hsu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6043-4132","authenticated-orcid":false,"given":"Pengcheng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.mcpro.2024.100804_bib1","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1007\/s44154-022-00054-1","article-title":"Root osmotic sensing from local perception to systemic responses","volume":"2","author":"Gorgues","year":"2022","journal-title":"Stress Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib2","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1038\/s41580-022-00479-6","article-title":"Plant hormone regulation of abiotic stress responses","volume":"23","author":"Waadt","year":"2022","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib3","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1146\/annurev-arplant-102820-095312","article-title":"Cell wall signaling in plant development and defense","volume":"73","author":"Wolf","year":"2022","journal-title":"Annu. Rev. Plant Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib4","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1111\/jipb.13228","article-title":"Ca2+ signaling in plant responses to abiotic stresses","volume":"64","author":"Dong","year":"2022","journal-title":"J.\u00a0Integr. Plant Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib5","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.cell.2016.08.029","article-title":"Abiotic stress signaling and responses in plants","volume":"167","author":"Zhu","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2024.100804_bib6","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/S0014-5793(96)01472-X","article-title":"An increase in cytosolic calcium ion concentration precedes hypoosmotic shock-induced activation of protein kinases in tobacco suspension culture cells","volume":"401","author":"Takahashi","year":"1997","journal-title":"FEBS Lett."},{"key":"10.1016\/j.mcpro.2024.100804_bib7","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1046\/j.1365-313X.1997.12051067.x","article-title":"Calcium signalling in Arabidopsis thaliana responding to drought and salinity","volume":"12","author":"Knight","year":"2003","journal-title":"Plant J."},{"key":"10.1016\/j.mcpro.2024.100804_bib8","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/nature13593","article-title":"OSCA1 mediates osmotic-stress-evoked Ca2+ increases vital for osmosensing in Arabidopsis","volume":"514","author":"Yuan","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.mcpro.2024.100804_bib9","doi-asserted-by":"crossref","first-page":"14309","DOI":"10.1073\/pnas.1900774116","article-title":"Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating","volume":"116","author":"Maity","year":"2019","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib10","doi-asserted-by":"crossref","first-page":"5060","DOI":"10.1038\/s41467-018-07564-5","article-title":"Structure of the hyperosmolality-gated calcium-permeable channel OSCA1.2","volume":"9","author":"Liu","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2024.100804_bib11","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.41844","article-title":"OSCA\/TMEM63 are an evolutionarily conserved family of mechanically activated ion channels","volume":"7","author":"Murthy","year":"2018","journal-title":"Elife"},{"key":"10.1016\/j.mcpro.2024.100804_bib12","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.41845","article-title":"Cryo-EM structure of the mechanically activated ion channel OSCA1.2","volume":"7","author":"Jojoa-Cruz","year":"2018","journal-title":"Elife"},{"key":"10.1016\/j.mcpro.2024.100804_bib13","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/s41586-020-2702-1","article-title":"The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity","volume":"585","author":"Thor","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.mcpro.2024.100804_bib14","doi-asserted-by":"crossref","first-page":"4815","DOI":"10.1016\/j.cub.2020.09.016","article-title":"BONZAI proteins control global osmotic stress responses in plants","volume":"30","author":"Chen","year":"2020","journal-title":"Curr. Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib15","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1111\/jipb.13061","article-title":"Protein kinases in plant responses to drought, salt, and cold stress","volume":"63","author":"Chen","year":"2021","journal-title":"J.\u00a0Integr. Plant Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib16","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1104\/pp.122.4.1355","article-title":"Calcium-independent activation of salicylic acid-induced protein kinase and a 40-kilodalton protein kinase by hyperosmotic stress","volume":"122","author":"Hoyos","year":"2000","journal-title":"Plant Physiol."},{"key":"10.1016\/j.mcpro.2024.100804_bib17","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/S0014-5793(02)03162-9","article-title":"Different protein kinase families are activated by osmotic stresses in Arabidopsis thaliana cell suspensions. Involvement of the MAP kinases AtMPK3 and AtMPK6","volume":"527","author":"Droillard","year":"2002","journal-title":"FEBS Lett."},{"key":"10.1016\/j.mcpro.2024.100804_bib18","doi-asserted-by":"crossref","first-page":"41758","DOI":"10.1074\/jbc.M405259200","article-title":"Identification of nine sucrose nonfermenting 1-related protein kinases 2 activated by hyperosmotic and saline stresses in Arabidopsis thaliana","volume":"279","author":"Boudsocq","year":"2004","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.mcpro.2024.100804_bib19","doi-asserted-by":"crossref","first-page":"E6388","DOI":"10.1073\/pnas.1511238112","article-title":"Plant Raf-like kinase integrates abscisic acid and hyperosmotic stress signaling upstream of SNF1-related protein kinase2","volume":"112","author":"Saruhashi","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib20","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/s41467-020-14477-9","article-title":"A\u00a0RAF-SnRK2 kinase cascade mediates early osmotic stress signaling in higher plants","volume":"11","author":"Lin","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2024.100804_bib21","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1111\/tpj.14756","article-title":"Arabidopsis Raf-like kinases act as positive regulators of subclass III SnRK2 in osmostress signaling","volume":"103","author":"Katsuta","year":"2020","journal-title":"Plant J."},{"key":"10.1016\/j.mcpro.2024.100804_bib22","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1038\/s41467-020-15239-3","article-title":"Plant Raf-like kinases regulate the mRNA population upstream of ABA-unresponsive SnRK2 kinases under drought stress","volume":"11","author":"Soma","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2024.100804_bib23","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/S1360-1385(02)02302-6","article-title":"Mitogen-activated protein kinase cascades in plants: a new nomenclature","volume":"7","author":"Group","year":"2002","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.mcpro.2024.100804_bib24","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.cell.2023.11.021","article-title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","volume":"187","author":"Kuhn","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2024.100804_bib25","doi-asserted-by":"crossref","DOI":"10.1016\/j.tplants.2024.04.004","article-title":"Emerging multiple function of B-RAFs in plants","volume":"29","author":"Wang","year":"2024","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.mcpro.2024.100804_bib26","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1073\/pnas.1018367108","article-title":"Arabidopsis decuple mutant reveals the importance of SnRK2 kinases in osmotic stress responses in\u00a0vivo","volume":"108","author":"Fujii","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib27","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.2003509","article-title":"Genetics and phosphoproteomics reveal a protein phosphorylation network in the abscisic acid signaling pathway in Arabidopsis thaliana","volume":"6","author":"Umezawa","year":"2013","journal-title":"Sci. Signal."},{"key":"10.1016\/j.mcpro.2024.100804_bib28","doi-asserted-by":"crossref","first-page":"11205","DOI":"10.1073\/pnas.1308974110","article-title":"Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action","volume":"110","author":"Wang","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib29","doi-asserted-by":"crossref","first-page":"3270","DOI":"10.1073\/pnas.1919901117","article-title":"Mapping proteome-wide targets of protein kinases in plant stress responses","volume":"117","author":"Wang","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib30","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/pcp\/pcz230","article-title":"The Sucrose Non-Fermenting 1-Related Protein Kinase 2 (SnRK2) Genes are multifaceted players in plant growth, development and response to environmental stimuli","volume":"61","author":"Mao","year":"2020","journal-title":"Plant Cell Physiol."},{"key":"10.1016\/j.mcpro.2024.100804_bib31","doi-asserted-by":"crossref","first-page":"8380","DOI":"10.1073\/pnas.0903144106","article-title":"Arabidopsis mutant deficient in 3 abscisic acid-activated protein kinases reveals critical roles in growth, reproduction, and stress","volume":"106","author":"Fujii","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib32","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1038\/nature08599","article-title":"In\u00a0vitro reconstitution of an abscisic acid signalling pathway","volume":"462","author":"Fujii","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.mcpro.2024.100804_bib33","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1089\/omi.2011.0091","article-title":"SnRK2 protein kinases\u2014key regulators of plant response to abiotic stresses","volume":"15","author":"Kulik","year":"2011","journal-title":"OMICS"},{"key":"10.1016\/j.mcpro.2024.100804_bib34","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1105\/tpc.106.048538","article-title":"Identification of two protein kinases required for abscisic acid regulation of seed germination, root growth, and gene expression in Arabidopsis","volume":"19","author":"Fujii","year":"2007","journal-title":"Plant Cell"},{"key":"10.1016\/j.mcpro.2024.100804_bib35","doi-asserted-by":"crossref","first-page":"3089","DOI":"10.1105\/tpc.007906","article-title":"Arabidopsis OST1 protein kinase mediates the regulation of stomatal aperture by abscisic acid and acts upstream of reactive oxygen species production","volume":"14","author":"Mustilli","year":"2002","journal-title":"Plant Cell"},{"key":"10.1016\/j.mcpro.2024.100804_bib36","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1104\/pp.113.222547","article-title":"Vacuolar transport of abscisic acid glucosyl ester is mediated by ATP-binding cassette and proton-antiport mechanisms in Arabidopsis","volume":"163","author":"Burla","year":"2013","journal-title":"Plant Physiol."},{"key":"10.1016\/j.mcpro.2024.100804_bib37","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1126\/science.1172408","article-title":"Regulators of PP2C phosphatase activity function as abscisic acid sensors","volume":"324","author":"Ma","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.mcpro.2024.100804_bib38","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1126\/science.1173041","article-title":"Abscisic acid inhibits type 2C protein phosphatases via the PYR\/PYL family of START proteins","volume":"324","author":"Park SY","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.mcpro.2024.100804_bib39","doi-asserted-by":"crossref","first-page":"2456","DOI":"10.1038\/s41467-021-22812-x","article-title":"Initiation and amplification of SnRK2 activation in abscisic acid signaling","volume":"12","author":"Lin","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2024.100804_bib40","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1038\/s41467-019-13875-y","article-title":"MAP3Kinase-dependent SnRK2-kinase activation is required for abscisic acid signal transduction and rapid osmotic stress response","volume":"11","author":"Takahashi","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2024.100804_bib41","doi-asserted-by":"crossref","first-page":"6184","DOI":"10.1038\/s41467-020-19977-2","article-title":"Role of Raf-like kinases in SnRK2 activation and osmotic stress response in plants","volume":"11","author":"Fabregas","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2024.100804_bib42","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/dnares\/dsq011","article-title":"In silico analysis reveals 75 members of mitogen-activated protein kinase kinase kinase gene family in rice","volume":"17","author":"Rao","year":"2010","journal-title":"DNA Res."},{"key":"10.1016\/j.mcpro.2024.100804_bib43","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1111\/tpj.15067","article-title":"Signaling mechanisms in abscisic acid-mediated stomatal closure","volume":"105","author":"Hsu","year":"2020","journal-title":"Plant J."},{"key":"10.1016\/j.mcpro.2024.100804_bib44","doi-asserted-by":"crossref","first-page":"2122","DOI":"10.1111\/jipb.13536","article-title":"Cell type-specific proteomics uncovers a RAF15-SnRK2.6\/OST1 kinase cascade in guard cells","volume":"65","author":"Wang","year":"2023","journal-title":"J.\u00a0Integr. Plant Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib45","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2107280118","article-title":"Raf-like kinases and receptor-like (pseudo)kinase GHR1 are required for stomatal vapor pressure difference response","volume":"118","author":"Hsu","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib46","doi-asserted-by":"crossref","first-page":"R204","DOI":"10.1016\/j.cub.2024.01.024","article-title":"Plant physiology: RAF kinases claim a conserved role in rapid auxin responses","volume":"34","author":"Wang","year":"2024","journal-title":"Curr. Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib47","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.3390\/cells10092180","article-title":"The multifaceted regulation of SnRK2 kinases","volume":"10","author":"Maszkowska","year":"2021","journal-title":"Cells"},{"key":"10.1016\/j.mcpro.2024.100804_bib48","doi-asserted-by":"crossref","first-page":"2328","DOI":"10.1093\/plcell\/koae073","article-title":"OPEN STOMATA1 phosphorylates CYCLIC NUCLEOTIDE-GATED CHANNELs to trigger Ca2+ signaling for ABA-induced stomatal closure in Arabidopsis","volume":"36","author":"Yang","year":"2024","journal-title":"Plant Cell"},{"key":"10.1016\/j.mcpro.2024.100804_bib49","doi-asserted-by":"crossref","first-page":"3340","DOI":"10.1016\/j.celrep.2018.05.044","article-title":"Arabidopsis duodecuple mutant of PYL ABA receptors reveals PYL repression of ABA-Independent SnRK2 activity","volume":"23","author":"Zhao","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.mcpro.2024.100804_bib50","doi-asserted-by":"crossref","first-page":"12232","DOI":"10.1021\/acs.analchem.3c00786","article-title":"Suspension trapping-based sample preparation workflow for In-Depth plant phosphoproteomics","volume":"95","author":"Chen","year":"2023","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2024.100804_bib51","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1021\/ac4031175","article-title":"Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography","volume":"86","author":"Tsai","year":"2014","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2024.100804_bib52","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1074\/mcp.TIR118.000702","article-title":"Universal plant phosphoproteomics workflow and its application to tomato signaling in response to cold stress","volume":"17","author":"Hsu","year":"2018","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.mcpro.2024.100804_bib53","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1074\/mcp.M114.044305","article-title":"Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues","volume":"14","author":"Bruderer","year":"2015","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.mcpro.2024.100804_bib54","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1038\/nmeth.3901","article-title":"The Perseus computational platform for comprehensive analysis of (prote)omics data","volume":"13","author":"Tyanova","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.mcpro.2024.100804_bib55","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1038\/s41467-020-14609-1","article-title":"Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries","volume":"11","author":"Bekker-Jensen","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2024.100804_bib56","doi-asserted-by":"crossref","first-page":"W122","DOI":"10.1093\/nar\/gkx382","article-title":"agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update","volume":"45","author":"Tian","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mcpro.2024.100804_bib57","article-title":"REVIGO summarizes and visualizes long lists of gene ontology terms","volume":"6","author":"Gibas","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.mcpro.2024.100804_bib58","doi-asserted-by":"crossref","first-page":"W216","DOI":"10.1093\/nar\/gkac194","article-title":"DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)","volume":"50","author":"Sherman","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mcpro.2024.100804_bib59","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2--approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.mcpro.2024.100804_bib60","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2016","journal-title":"Methods Ecol. Evol."},{"key":"10.1016\/j.mcpro.2024.100804_bib61","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gky1063","article-title":"iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains","volume":"47","author":"Guo","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mcpro.2024.100804_bib62","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1111\/j.1365-313X.2010.04281.x","article-title":"Phospho-site mapping, genetic and in planta activation studies reveal key aspects of the different phosphorylation mechanisms involved in activation of SnRK2s","volume":"63","author":"Vlad","year":"2010","journal-title":"Plant J."},{"key":"10.1016\/j.mcpro.2024.100804_bib63","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1104\/pp.105.061275","article-title":"Osmotic signaling in plants: multiple pathways mediated by emerging kinase families","volume":"138","author":"Boudsocq","year":"2005","journal-title":"Plant Physiol."},{"key":"10.1016\/j.mcpro.2024.100804_bib64","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1126\/science.1215106","article-title":"Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases","volume":"335","author":"Soon FF","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.mcpro.2024.100804_bib65","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1093\/plphys\/kiaa046","article-title":"Activation of SnRK2 by Raf-like kinase ARK represents a primary mechanism of ABA and abiotic stress responses","volume":"185","author":"Islam","year":"2021","journal-title":"Plant Physiol."},{"key":"10.1016\/j.mcpro.2024.100804_bib66","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1104\/pp.16.01825","article-title":"Reconstitution of abscisic acid signaling from the receptor to DNA via bHLH transcription factors","volume":"174","author":"Takahashi","year":"2017","journal-title":"Plant Physiol."},{"key":"10.1016\/j.mcpro.2024.100804_bib67","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.molp.2015.10.003","article-title":"A\u00a0direct Link between abscisic acid sensing and the chromatin-remodeling ATPase BRAHMA via core ABA signaling pathway components","volume":"9","author":"Peirats-Llobet","year":"2016","journal-title":"Mol. Plant"},{"key":"10.1016\/j.mcpro.2024.100804_bib68","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/j.molcel.2017.12.002","article-title":"Reciprocal regulation of the TOR kinase and ABA receptor balances plant growth and stress response","volume":"69","author":"Wang","year":"2018","journal-title":"Mol. Cell"},{"key":"10.1016\/j.mcpro.2024.100804_bib69","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1111\/jipb.13240","article-title":"How long should a kiss last between a kinase and its substrate?","volume":"64","author":"Zhu","year":"2022","journal-title":"J.\u00a0Integr. Plant Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib70","doi-asserted-by":"crossref","DOI":"10.1038\/nplants.2016.204","article-title":"ABA-unresponsive SnRK2 protein kinases regulate mRNA decay under osmotic stress in plants","volume":"3","author":"Soma","year":"2017","journal-title":"Nat. Plants"},{"key":"10.1016\/j.mcpro.2024.100804_bib71","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1104\/pp.19.00818","article-title":"SnRK2 protein kinases and mRNA decapping machinery control root development and response to salt","volume":"182","author":"Kawa","year":"2020","journal-title":"Plant Physiol."},{"key":"10.1016\/j.mcpro.2024.100804_bib72","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/s41477-021-01040-7","article-title":"Phosphorylation of SWEET sucrose transporters regulates plant root:shoot ratio under drought","volume":"8","author":"Chen","year":"2022","journal-title":"Nat. Plants"},{"key":"10.1016\/j.mcpro.2024.100804_bib73","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1111\/j.1365-313X.2005.02583.x","article-title":"Abscisic acid-activated SNRK2 protein kinases function in the gene-regulation pathway of ABA signal transduction by phosphorylating ABA response element-binding factors","volume":"44","author":"Kobayashi","year":"2005","journal-title":"Plant J."},{"key":"10.1016\/j.mcpro.2024.100804_bib74","doi-asserted-by":"crossref","first-page":"2982","DOI":"10.1016\/j.febslet.2009.08.033","article-title":"Phosphorylation of the Arabidopsis AtrbohF NADPH oxidase by OST1 protein kinase","volume":"583","author":"Sirichandra","year":"2009","journal-title":"FEBS Lett."},{"key":"10.1016\/j.mcpro.2024.100804_bib75","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005835","article-title":"Type One Protein Phosphatase 1 and its regulatory protein inhibitor 2 negatively regulate ABA signaling","volume":"12","author":"Hou","year":"2016","journal-title":"PLoS Genet."},{"key":"10.1016\/j.mcpro.2024.100804_bib76","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2100073118","article-title":"Arabidopsis group C Raf-like protein kinases negatively regulate abscisic acid signaling and are direct substrates of SnRK2","volume":"118","author":"Kamiyama","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib77","doi-asserted-by":"crossref","DOI":"10.15252\/embr.202255037","article-title":"The plant FYVE domain-containing protein FREE1 associates with microprocessor components to repress miRNA biogenesis","volume":"24","author":"Li","year":"2023","journal-title":"EMBO Rep."},{"key":"10.1016\/j.mcpro.2024.100804_bib78","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1038\/cr.2008.300","article-title":"MEKK1, MKK1\/MKK2 and MPK4 function together in a mitogen-activated protein kinase cascade to regulate innate immunity in plants","volume":"18","author":"Gao","year":"2008","journal-title":"Cell Res."},{"key":"10.1016\/j.mcpro.2024.100804_bib79","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1093\/mp\/ssn079","article-title":"A\u00a0major role of the MEKK1\u2013MKK1\/2\u2013MPK4 pathway in ROS signalling","volume":"2","author":"Pitzschke","year":"2009","journal-title":"Mol. Plant"},{"key":"10.1016\/j.mcpro.2024.100804_bib80","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1111\/tpj.13737","article-title":"Maternal control of embryogenesis by MPK6 and its upstream MKK4\/MKK5 in Arabidopsis","volume":"92","author":"Zhang","year":"2017","journal-title":"Plant J."},{"key":"10.1016\/j.mcpro.2024.100804_bib81","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.pbi.2018.04.012","article-title":"Conveying endogenous and exogenous signals: MAPK cascades in plant growth and defense","volume":"45","author":"Zhang","year":"2018","journal-title":"Curr. Opin. Plant Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib82","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1126\/science.1162263","article-title":"Arabidopsis stomatal initiation is controlled by MAPK-mediated regulation of the bHLH SPEECHLESS","volume":"322","author":"Lampard GR","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.mcpro.2024.100804_bib83","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1126\/science.1096014","article-title":"Stomatal development and pattern controlled by a MAPKK kinase","volume":"304","author":"Bergmann","year":"2004","journal-title":"Science"},{"key":"10.1016\/j.mcpro.2024.100804_bib84","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.3389\/fpls.2020.01220","article-title":"Expanding the mitogen-activated protein kinase (MAPK) universe: an update on MAP4Ks","volume":"11","author":"Pan","year":"2020","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.mcpro.2024.100804_bib85","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s12859-016-1433-7","article-title":"KinMap: a web-based tool for interactive navigation through human kinome data","volume":"18","author":"Eid","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.mcpro.2024.100804_bib86","doi-asserted-by":"crossref","first-page":"2142","DOI":"10.1105\/tpc.105.032508","article-title":"Calcium: a central regulator of plant growth and development","volume":"17","author":"Hepler","year":"2005","journal-title":"Plant Cell"},{"key":"10.1016\/j.mcpro.2024.100804_bib87","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/s41438-019-0117-7","article-title":"EGTA reduces the inflorescence stem mechanical strength of herbaceous peony by modifying secondary wall biosynthesis","volume":"6","author":"Tang","year":"2019","journal-title":"Hortic. Res."},{"key":"10.1016\/j.mcpro.2024.100804_bib88","doi-asserted-by":"crossref","first-page":"10655","DOI":"10.1074\/jbc.M006989200","article-title":"An apoplastic Ca2+ sensor regulates internal Ca2+ release in aequorin-transformed tobacco cells","volume":"276","author":"Cessna","year":"2001","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.mcpro.2024.100804_bib89","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1016\/j.devcel.2012.02.015","article-title":"Genetic framework of cyclin-dependent kinase function in Arabidopsis","volume":"22","author":"Nowack","year":"2012","journal-title":"Dev. Cell"},{"key":"10.1016\/j.mcpro.2024.100804_bib90","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.pbi.2015.12.003","article-title":"Integration of developmental and environmental signals into cell proliferation and differentiation through RETINOBLASTOMA-RELATED 1","volume":"29","author":"Harashima","year":"2016","journal-title":"Curr. Opin. Plant Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib91","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/0012-1606(83)90252-X","article-title":"Calcium antagonists and calmodulin inhibitors block cytokinin-induced bud formation in Funaria","volume":"99","author":"Saunders","year":"1983","journal-title":"Dev. Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib92","doi-asserted-by":"crossref","first-page":"3502","DOI":"10.5586\/asbp.3502","article-title":"EGTA, a calcium chelator, affects cell cycle and increases DNA methylation in root tips of Triticum aestivum L","volume":"85","author":"Zhang","year":"2016","journal-title":"Acta Soc. Bot. Pol."},{"key":"10.1016\/j.mcpro.2024.100804_bib93","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1016\/S0960-9822(00)00511-X","article-title":"Phosphorylation of the MEKK Ste11p by the PAK-like kinase Ste20p is required for MAP kinase signaling in\u00a0vivo","volume":"10","author":"Drogen","year":"2000","journal-title":"Curr. Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib94","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1016\/S0962-8924(01)01980-8","article-title":"The Ste20 group kinases as regulators of MAP kinase cascades","volume":"11","author":"Dan","year":"2001","journal-title":"Trends Cell Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib95","doi-asserted-by":"crossref","first-page":"4395","DOI":"10.1074\/jbc.M110000200","article-title":"Interaction between active Pak1 and Raf-1 is necessary for phosphorylation and activation of Raf-1","volume":"277","author":"Zang","year":"2002","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.mcpro.2024.100804_bib96","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1093\/jxb\/erv538","article-title":"The Hippo\/STE20 homolog SIK1 interacts with MOB1 to regulate cell proliferation and cell expansion in Arabidopsis","volume":"67","author":"Xiong","year":"2016","journal-title":"J.\u00a0Exp. Bot."},{"key":"10.1016\/j.mcpro.2024.100804_bib97","doi-asserted-by":"crossref","first-page":"2468","DOI":"10.15252\/embj.201694248","article-title":"The Arabidopsis CERK1-associated kinase PBL27 connects chitin perception to MAPK activation","volume":"35","author":"Yamada","year":"2016","journal-title":"EMBO J."},{"key":"10.1016\/j.mcpro.2024.100804_bib98","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1111\/nph.17573","article-title":"A\u00a0Phytophthora capsici RXLR effector targets and inhibits the central immune kinases to suppress plant immunity","volume":"232","author":"Liang","year":"2021","journal-title":"New Phytol."},{"key":"10.1016\/j.mcpro.2024.100804_bib99","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2116570118","article-title":"The small molecule Zaractin activates ZAR1-mediated immunity in Arabidopsis","volume":"118","author":"Seto","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2024.100804_bib100","doi-asserted-by":"crossref","DOI":"10.1038\/nplants.2017.27","article-title":"Expanded type III effector recognition by the ZAR1 NLR protein using ZED1-related kinases","volume":"3","author":"Seto","year":"2017","journal-title":"Nat. Plants"},{"key":"10.1016\/j.mcpro.2024.100804_bib101","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1111\/tpj.12535","article-title":"Selective regulation of the chitin-induced defense response by the Arabidopsis receptor-like cytoplasmic kinase PBL27","volume":"79","author":"Shinya","year":"2014","journal-title":"Plant J."},{"key":"10.1016\/j.mcpro.2024.100804_bib102","first-page":"83","article-title":"Calcium-regulated protein kinases of plants","volume":"16","author":"Harmon","year":"2003","journal-title":"Gravit. Space Biol. Bull."},{"key":"10.1016\/j.mcpro.2024.100804_bib103","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1093\/jxb\/err320","article-title":"Evidence that abscisic acid promotes degradation of SNF1-related protein kinase (SnRK) 1 in wheat and activation of a putative calcium-dependent SnRK2","volume":"63","author":"Coello","year":"2012","journal-title":"J.\u00a0Exp. Bot."},{"key":"10.1016\/j.mcpro.2024.100804_bib104","doi-asserted-by":"crossref","first-page":"3429","DOI":"10.1074\/jbc.M110.115535","article-title":"SNF1-related protein kinases 2 are negatively regulated by a plant-specific calcium sensor","volume":"286","author":"Bucholc","year":"2011","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.mcpro.2024.100804_bib105","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007429","article-title":"Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling","volume":"15","author":"Maheshwari","year":"2019","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.mcpro.2024.100804_bib106","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1002\/j.2769-2795.2021.tb00064.x","article-title":"Application prospects of cerebrospinal fluid DIA techniques in identifying key regulatory molecules for mental disorders in encephalitis","volume":"7","author":"Zhou","year":"2021","journal-title":"Ibrain"},{"key":"10.1016\/j.mcpro.2024.100804_bib107","doi-asserted-by":"crossref","DOI":"10.3390\/ijms222312856","article-title":"Data-independent acquisition-based proteome and phosphoproteome profiling reveals early protein phosphorylation and dephosphorylation events in Arabidopsis seedlings upon cold exposure","volume":"22","author":"Tan","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.mcpro.2024.100804_bib108","doi-asserted-by":"crossref","first-page":"2077","DOI":"10.1016\/j.scib.2023.08.017","article-title":"Data-independent acquisition-based global phosphoproteomics reveal the diverse roles of casein kinase 1 in plant development","volume":"68","author":"Qu","year":"2023","journal-title":"Sci. Bull. (Beijing)"},{"key":"10.1016\/j.mcpro.2024.100804_bib109","doi-asserted-by":"crossref","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences","volume":"50","author":"Perez-Riverol","year":"2022","journal-title":"Nucleic Acids Res."}],"container-title":["Molecular & Cellular Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S153594762400094X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S153594762400094X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T04:07:00Z","timestamp":1778818020000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S153594762400094X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8]]},"references-count":109,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,8]]}},"alternative-id":["S153594762400094X"],"URL":"https:\/\/doi.org\/10.1016\/j.mcpro.2024.100804","relation":{},"ISSN":["1535-9476"],"issn-type":[{"value":"1535-9476","type":"print"}],"subject":[],"published":{"date-parts":[[2024,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis","name":"articletitle","label":"Article Title"},{"value":"Molecular & Cellular Proteomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mcpro.2024.100804","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.","name":"copyright","label":"Copyright"}],"article-number":"100804"}}