Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05938_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05918_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05922_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05932_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05934_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05920_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05936_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05916_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05930_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05914_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05928_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/PRC-6765MP_UPRC_10090X05924_2p_Ionopticks24_PM4_Lambrecht_PTM_SPR6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/UPRC_10090.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077760/txt.zipprimaryOK200sahine.lameire@irc.vib-ugent.beTeresa Mendes MaiaData-dependent acquisitionMass SpectrometryPhospho-proteomicsSte20 kinaseTcr signalingNaïve t cellshttps://www.ebi.ac.uk/pride/archive/projects/PXD077760SpleenSpleens were mechanically dissociated through 70-µm cell strainers to obtain single-cell suspensions. Cells were incubated with fluorescently labelled monoclonal antibodies for 30 min at 4°C in the presence of anti-mouse FcγRII/III to reduce nonspecific binding. Dead cells were excluded using Fixable Viability Dye eFluor™ 780. Naïve CD8 T cells were purified through FACS sorting. Cells were pelleted by centrifugation and snap-frozen, then stored at −80 °C until further processing for proteomic analysis. Cell pellets were homogenized in 100 µl lysis buffer containing 4% sodium dodecyl sulfate and 50 mM Tris, pH 8.5. Next, the resulting lysate was transferred to a 96-well PIXUL plate and sonicated with a PIXUL Multisample sonicator for 5 min with default settings (Pulse 50 cycles, PRF 1 kHz, Burst Rate 20 Hz). Samples were centrifuged for 15 min at maximum speed at room temperature (RT) to remove insoluble components. Proteins were reduced and alkylated by addition of 10 mM Tris(2-carboxyethyl)phosphine hydrochloride and 40 mM chloroacetamide and incubation for 30 min at RT in the dark. Ethanol was added to the sample up to a final concentration of 55% and 1 mg washed Sera-Mag Magnetic Carboxylate Modified beads (hydrophilic:hydrophobic, 1:1, washed with water) were added to each sample. After capture of proteins for 30 min at RT and 800 rpm, beads were collected on a magnetic rack and supernatant was removed. After 3 washes with 80% ethanol, proteins were digested at 37°C and 800 rpm, first for 2h with lysyl endopeptidase and O/N with trypsin (both 1/100, w/w)). Digested peptides were recovered in 2 steps: first samples were mounted on a magnetic rack and supernatant was isolated, then MilliQ water was added to the beads, beads were sonicated in a waterbath for 15 min and supernatant was added to the first eluate, using a magnetic rack. Eluted peptides were acidified with formic acid (FA), cleared by centrifugation and transferred to new tubes. Peptides were dried, resuspended in a mixture of water/ACN/TFA (14:80:6, v/v/v) and used for phosphopeptide enrichment. Phosphopeptides were enriched with MagReSyn® Ti-IMAC beads following the protocol according to the manufacturer’s instructions with slight modifications. Briefly, 20 µl beads (per sample) were washed twice with 70% EtOH, once with 1% NH4OH and 3x with a mixture of water/ACN/TFA (14:80:6, v/v/v). Next, the digested sample was incubated with the washed beads for 30 min at RT, the beads were washed once with a mixture of water/ACN/TFA (14:80:6, v/v/v) and three times with a mixture of water/ACN/TFA (19:80:1, v/v/v). Phosphopeptides were eluted from the beads by adding three times 80 µl 1% NH4OH. 60 µl 10% FA was added to the combined eluate, samples were dried in a speedvac vacuum concentrator, redissolved in 0.1% TFA and desalted on a reversed phase (RP) C18 OMIX tip. The tip was first washed 3x with 100 µl pre-wash buffer (0.1% TFA in water/ ACN (20:80, v/v)) and pre-equilibrated 5 times with 100 µl of wash buffer (0.1% TFA in water) before the sample was loaded on the tip. After peptide binding, the tip was washed 3 times with 100 µl of wash buffer and peptides were eluted twice with 100 µl elution buffer (0.1% TFA in water/ACN (40:60, v/v)). The combined elutions were transferred to HPLC inserts and dried in a vacuum concentrator. Peptides were re-dissolved in loading solvent A (0.1% TFA in water/acetonitrile (ACN) (99.5:0.5, v/v)) of which 40% was injected on an Ultimate 3000 ProFlow nanoLC system in-line connected to a Orbitrap Exploris 240 mass spectrometer equipped with pneu-Nimbus dual ion source. Trapping was performed at 20 μl/min for 2 min in loading solvent A on a PepMap™ Neo Trap column (300 μm internal diameter (I.D.), 5 μm beads). The peptides were separated on a 250 mm Odyssey Ultimate, 1.7 µm C18, 75 µm inner diameter kept at a constant temperature of 45°C. Peptides were eluted by a gradient reaching 26,4 % MS solvent B (0.1% FA in acetonitrile) after 135 min, 44% MS solvent B at 155 min, 56% MS solvent B at 160 min followed by a 5-min wash at 56% MS solvent B and re-equilibration with MS solvent A (0.1% FA in water). The flow rate was set to 250 nl/min. The mass spectrometer was operated in data-dependent positive ionization mode, with a cycle time of 1 second. Full-scan MS spectra (350-1200 m/z) were acquired at a resolution of 120,000 in the Orbitrap analyzer after accumulation to a normalized AGC target value of 300% with a maximum injection time of 25 ms. The precursor ions were filtered for charge states (2-6 required), dynamic exclusion (30 s; +/- 10 ppm window, n=1) and intensity (minimal intensity of 8E3). The precursor ions were selected in the quadrupole with an isolation window of 2 m/z and accumulated to a normalized AGC target of 50% or a maximum injection time of 100 ms and activated using HCD fragmentation (30% NCE). The fragments were analysed in the Orbitrap at a resolution of 15,000 and first mass was set to 120.PrideNot availablePhospho-proteomics: LC-MS/MS runs of all 12 samples were searched together using the MaxQuant (Cox & Mann, 2008) algorithm (version 2.6.7.0 ) with mainly default search settings, including a false discovery rate set at 1% on precursor and protein level. Phosphorylation was specified as variable modification. Spectra were searched against the Mus musculus reference proteome, containing 21,701 protein entries. The mass tolerance for precursor and fragment ions was set to 4.5 and 20 ppm, respectively, during the main search. Enzyme specificity was set as C-terminal to arginine and lysine, also allowing cleavage at proline bonds with a maximum of two missed cleavages. Variable modifications were set to phosphorylation in serine, threonine or tyrosine, oxidation of methionine residues and acetylation of protein N-termini. Matching between runs was enabled with a matching time window of 0.7 minutes and an alignment time window of 20 minutes. Only proteins with at least one unique or razor peptide were retained. Proteins were quantified by the MaxLFQ algorithm integrated in the MaxQuant software.ProteomicsSahine LameireVIB Inflammation Research Center Ghent UniversityPARTIALMus Musculus (mouse)teresa.maia@vib-ugent.be10.3389/FIMMU.2026.1838764VIB Proteomics CoreBelgiumfalseTAOK3 controls naïve T cell homeostasisGenetic deletion or kinase inactivation of TAOK3 resulted in a profound, cell-intrinsic loss of naive CD8⁺ T cells. Despite enhanced sensitivity to TCR ligation and enhanced downstream signalling, proliferating CD8⁺ T cells did not survive in vitro and anti-viral CD8⁺ T cell immunity was compromised in vivo in the absence of TAOK3. To delineate the molecular pathways governed by TAOK3, we performed an unbiased phosphoproteomic analysis of Taok3-deficient 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