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Hothorn"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073452"],"sample_protocol":["Protein samples were loaded on a mini polyacrylamide gel, migrated and stained by Coomassie Blue. Gel bands were excised and digested with sequencing-grade trypsin (Promega, Madison, WI, USA, Product N. V5111) or chymotrypsin (Promega, Prod.N. V1061) essentially as described (Shevchenko, et al., 2006). Extracted tryptic peptides were dried and resuspended in 0.1% formic acid, 2% (v/v) acetonitrile.  LC-MS/MS protocol for first part “Quantitative phosphoproteomics of protein kinases”: LC-MS/MS analyses were carried out on a TIMS-TOF Pro (Bruker, Bremen, Germany) mass spectrometer interfaced through a nanospray ion source (“captive spray”) to an Ultimate 3000 RSLCnano HPLC system (Dionex). Peptides were separated on a reversed-phase custom packed 45 cm C18 column (75 μm ID, 100Å, Reprosil Pur 1.9 um particles, Dr. Maisch, Germany) at a flow rate of 250 nl/min with a 2-27% acetonitrile gradient in 33 min followed by a ramp to 45% in 5 min and to 90% in 5 min (total method time: 65 min, all solvents contained 0.1% formic acid). Data-dependent acquisition was carried out using a standard TIMS PASEF method (Meier, et al., 2018) with ion accumulation for 100 ms for each the survey MS1 scan and the TIMS-coupled MS2 scans. Duty cycle was kept at 100%. Up to 10 precursors were targeted per TIMS scan. Precursor isolation was done with a 2 or 3 m/z windows below or above m/z 800, respectively. The minimum threshold intensity for precursor selection was 2500.  If the inclusion list allowed it, precursors were targeted more than one time to reach a minimum target total intensity of 20’000. Collision energy was ramped linearly based uniquely on the 1/k0 values from 20 (at 1/k0=0.6) to 59 eV (at 1/k0=1.6). Total duration of a scan cycle including one survey and 10 MS2 TIMS scans was 1.16 s. Precursors could be targeted again in subsequent cycles if their signal increased by a factor 4.0 or more.  After selection in one cycle, precursors were excluded from further selection for 60s. Mass resolution in all MS measurements was approximately 35’000.  LC-MS/MS protocol for second part “Identification of phosphosites in kinases and phosphatases”: Data-dependent LC-MS/MS analyses of samples were carried out on a Fusion Tribrid Orbitrap mass spectrometer (Thermo Fisher Scientific) interfaced through a nano-electrospray ion source to an Ultimate 3000 RSLCnano HPLC system (Dionex). Peptides were separated on a reversed-phase custom packed 45 cm C18 column (75 μm ID, 100Å, Reprosil Pur 1.9 um particles, Dr. Maisch, Germany) with a 4-90% acetonitrile gradient in 0.1% formic acid at a flow rate of 250 nl/min (total time 140 min). Full MS survey scans were performed at 120'000 resolution. A data-dependent acquisition method controlled by Xcalibur software (Thermo Fisher Scientific) was used that optimized the number of precursors selected (“top speed”) of charge 2+ to 5+ while maintaining a fixed scan cycle of 0.6 s. Peptides were fragmented by higher energy collision dissociation (HCD) with a normalized energy of 32%. The precursor isolation window used was 1.6 Th, and the MS2 scans were done in the ion trap. The m/z of fragmented precursors was then dynamically excluded from selection during 60 s."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Data processing protocol for first part “Quantitative phosphoproteomics of protein kinases”: Scaffold (version Scaffold 5.0.0, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications. Peptide identifications were accepted if they could be established at greater than 80.0% probability by the Percolator posterior error probability calculation (Käll, et al. 2008, Bioinformatics 24(16): i42-8). Protein identifications were accepted if they could be established at greater than 95.0% probability and contained at least 2 identified peptides.  Protein probabilities were assigned by the Protein Prophet algorithm (Nesvizhskii, et al. 2003, Anal. Chem. 75 (17): 4646-58).  All phosphopeptide identifications and phosphosite localizations reported were manually  validated.   Data processing protocol for second part “Identification of phosphosites in kinases and phosphatases”: MS data were analyzed using Mascot 2.8 (Matrix Science, London, UK) set up to search the Arabidopsis_thaliana reference proteome based on the UniProt database (www.uniprot.org, version of August 24th, 2020, containing 39’347  sequences), and a custom contaminant database containing the most usual environmental contaminants and enzymes used for digestion (keratins, trypsin, etc, 351 sequences). In a second pass search, the sequence of the expressed tagged proteins was searched alone, together with the contaminant database, and the matched peptides were used for peptide quantitation. Trypsin (cleavage C-terminal to K,R) , allowing 2 missed cleavages and  Chymotrypsin (cleavage C-terminal to Phe, Leu, Trp, Tyr, semispecific) were used as the enzyme definitions. Mascot was searched with a parent ion tolerance of 15 ppm and a fragment ion mass tolerance of 0.5 Da. Carbamidomethylation of cysteine was specified in Mascot as a fixed modification.  Protein N-terminal acetylation, methionine oxidation and phosphorylation on Ser, Thr and Tyr were specified as variable modifications. Based on Mascot results, the MsViz software (Martin-Campos, et al. 2017, J. Proteome Res 16(8): 3092–3101) was used to manually quantify and compare intensities of phosphorylation sites in the BSU1 sequence. Reference unmodified peptides were used for normalizing protein amounts when necessary."],"omics_type":["Proteomics"],"labhead":["Michael Hothorn"],"instrument_platform":[""],"labhead_affiliation":["Structural Plant Biology Laboratory, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland"],"submission_type":["COMPLETE"],"species":["Arabidopsis Thaliana (mouse-ear Cress)"],"publication":["42166246 Rico-Resendiz F, Pri-Tal O, Raia P, Moretti A, Chen H, Yu J, Broger L, Fuchs C, Hothorn LA, Loubéry S, Hothorn M. Plant Kelch phosphatases are Ser/Thr phosphatases involved in cell cycle regulation.  Proc Natl Acad Sci U S A. 2026 123(21):e2600591123 10.1073/pnas.2600591123"],"submitter_mail":["michael.hothorn@unige.ch"],"submitter_affiliation":["Department of Plant Science, University of Geneva"],"submitter_country":["Switzerland"],"doi":["10.6019/PXD073452"],"additional_accession":[]},"is_claimable":false,"name":"Identification of phosphorylations sites in Arabidopsis thaliana BSU1 recombinantly expressed in insect cells, and when incubated with the GSK3 kinase BIN2.","description":"Brassinosteroids (BRs) are plant steroid hormones sensed at the cell surface by the membrane receptor kinase BRI1. Activation of BRI1 leads to the dephosphorylation of BZR1/BES1 transcription factors through inactivation of the glycogen synthase kinase 3 BIN2. Here, the in vitro phosphorylation sites of the isolated BSU1 Kelch domain (residues 11-351), phosphatase domain (residues 421-793) and of full-length BSU1 (residues 1-793) recombinantly expressed in baculovirus-infected Spodoptera frugiperda cells were identified in isolation (labelled ctrl) or after incubation with the GSK3 kinase BIN2, expressed as a thioredoxin A fusion protein in E. coli. Reactions were performed in the presence of 100 micromolar ATP and 1 mM MgCl2 for 1:30 h at room temperature.","dates":{"publication":"2026-05-22","submission":"2026-01-23"},"accession":"PXD073452","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:1211601","NEWT:876138","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:391619","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NEWT:13164","NEWT:216129","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:1194669","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:8479","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:630","NEWT:334747","NEWT:61235","NEWT:15368","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:469008","NEWT:260707","NEWT:256318","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863",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