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CernyData-dependent acquisitionMass SpectrometryBottom-up proteomicshttps://www.ebi.ac.uk/pride/archive/projects/PXD065957LeafThe extraction of proteins from lyophilized tissues was conducted according to the protocol delineated by (Berková et al. 2023). In brief, tissue samples underwent homogenization, and aliquots ranging between 10-20 mg were lyophilized. Subsequently, these were extracted utilizing a mixture of tert-butyl methyl ether and methanol (3:1 ratio). The precipitated protein pellets were then resolubilized in a solution composed of 8 M urea, 10 mM dithiothreitol (DTT), and 100 mM ammonium bicarbonate. Following solubilization, the proteins underwent alkylation and were digested with trypsin. Each sample, containing precisely 5 µg of peptides, was subjected to analysis via nanoflow reverse-phase liquid chromatography coupled with mass spectrometry (LC-MS/MS). The chromatographic separation was achieved using a 25 cm bioZen 2.6 µm Peptide XB-C18 (Phenomenex) column interfaced with a Dionex Ultimate 3000 RSLC nano-UPLC and an Orbitrap Fusion Lumos Tribrid Mass Spectrometer, equipped with a FAIMS Pro Interface (Thermo Fisher Scientific, Waltham, MA, USA). The analysis utilized alternating FAIMS compensation voltages of −40, −50, and −75 V.PrideThe acquired MS/MS spectra were subsequently recalibrated and interrogated against the Araport 11 protein database, alongside a database of common contaminants, using Proteome Discoverer 2.5. Algorithms Sequest HT, MS Amanda 2.0, and MSFragger facilitated the search. Quantitative analysis was restricted to proteins identified by at least two unique peptides.ProteomicsMartin CernyMendel University in BrnoPARTIALArabidopsis Thaliana (mouse-ear Cress)martincerny83@gmail.com10.1016/J.PLAPHY.2026.111402Mendel University in BrnoCzech RepublicfalseDevelopment-dependent response in cytokinin signaling mutants under drought stressLeaf proteome provides evidence of contrasting development-dependent response in cytokinin signaling mutants under drought 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