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SalomonMass SpectrometryBottom-up proteomicshttps://www.ebi.ac.uk/pride/archive/projects/PXD069485T CellJurkat Cell2.7.1 Reduction, alkylation, trypsinization and desalting Eleven milligrams of total protein were taken for each sample, then samples were adjusted to an equivalent volume (4.45 mL, ~1.6 M Urea final) with 20 mM HEPES, then reduced with 10 mM dithiothreitol (final) for 30 minutes at 37 C, then alkylated with 10 mM iodoacetamide (final) for 15 minutes in the dark. In solution trypsinisation was initiated with addition of Sequencing Grade Trypsin (Promega #V5113) at a ratio of 1:100 trypsin:protein. After trypsinisation, samples were acidified to 1% trifluoroacetic acid (TFA), then cleared by centrifugation. Samples were desalted using Waters C18 vacuum columns as previously described(Callahan, Mojumdar, et al. 2025). Under low vacuum, columns were activated using 100% acetonitrile (ACN), then equilibrated with 2 washes of 0.1% TFA. Samples were then passed through the columns, trapping peptides, then washed three times with 1, 5, and 6 mL of 0.1% TFA, before elution with 40% TFA, 0.1% ACN. After elution, 10 pmol of a phosphotyrosine standard (LIEDpYTAK) was added to each sample, then each sample was diluted to 20% ACN before freezing and 48 hour lyophilisation. 2.7.2 pY enrichment with Src SH2 superbinder Phosphotyrosine enrichment using recombinant Src SH2 superbinder (sSH2) was performed as previously described(Callahan, Puterbaugh, et al. 2025; Callahan, Mojumdar, et al. 2025; Griffith et al. 2022; Callahan et al. 2024; n.d.). Briefly, ~11 mg of dried peptide was resuspended in ice cold IAP buffer (10 mM sodium phosphate monobasic monohydrate, 50 mM sodium chloride, 50 mM morpholinopropanesulfonic) at room temperature for 30 minutes with brief, interspersed vortexing. One hundred micrograms of sSH2 conjugated to agarose beads was aliquotted into microcentrifuge tubes, then washed 3 times (1,500 xg, 2 min to collect beads) with 1 mL of ice cold IAP buffer before addition of sample for 2 hours at 4 C on an end over end rotator. After pY peptide binding, beads were washed 2 times with 1 mL ice cold IAP buffer, then 3 times with ice cold HPLC water. After the last water wash, all of the liquid was removed from the beads using an insulin syringe. Phosphotyrosine peptides were eluted from the beads using 0.15% TFA on a thermomixer at 1,150 rpm for 10 minutes, twice. Eluted pY peptides were then desalted using Empore C18 StageTips as previously described(Callahan, Mojumdar, et al. 2025) and dried by speed-vac before LC-MS/MS acquisition. 2.7.3 LC-MS/MS acquisition Samples were separated as previously described(Callahan, Puterbaugh, et al. 2025; Callahan, Mojumdar, et al. 2025) on a Vanquish Neo uHPLC system with an Acclaim PepMap C18 Trap column (7 cm, 2 cm bed length, 3 μm particle size, 100 A) and IonOpticks Aurora Ultimate (25 cm long x 75 μm ID, 1.7 μm particle size) and acquired on an Orbitrap Ascend mass spectrometer (Thermo Fisher). The separation gradient started at 5% Solvent B (80% ACN, 0.1% Formic Acid [FA])/95% Solvent A (0.1% FA) and increased to 30% Solvent B over 50 minutes, then spiked to 99% Solvent B for the remaining 5 minutes of acquisition. After acquisition, the flow path was washed with 4 alternating zebra washes, alternating between 100% Solvent A and 100% Solvent B before being reequilibrated for the next run. The spray voltage was 2050 V, with an ion transfer tube temperature of 275 C, and a lock-mass of 445.12003. For MS1 acquisition, wide quant isolation on the orbitrap detector at a resolution of 120,000 with a mass range of 300-1500 m/z was used. The maximum injection time was 50 ms, normalised AGC target was 250%, and RF lens was set to 30%, and data collection was in centroid mode. The following filters were included: monoisotopic peak and peptide mode, Charge state (+2-+7), Precursor Selection Range (375-1,500 m/z), Dynamic Exclusion (exclude after 1 time, 15 sec exclusion time, 10ppm low and high mass tolerance, excluding isotopes), Intensity Threshold (intensity range of 20000 (min) – 1E20 (max) with relative intensity threshold of 20%). MS2 spectra were acquired in data dependent mode with a cycle time of 3 seconds, normalised HCD fragmentation energy of 30%, and a 0.7 m/s quadrupole isolation window. Peptide fragments were detected using the ion trap detector with Turbo Mode active (scan range 150-2000 m/z) in centroid mode with the following settings: 35 ms maximum injection time, 100% normalised AGC target, dynamic maximum injection time active.Pride2.7.4 Database searching and relative abundance quantification .RAW files from the mass spectrometer were searched as previously described using the High Throughput Autonomous Proteomics Pipeline(Yu and Salomon 2010) and PeptideDepot(Yu and Salomon 2009). MS2 spectra were searched using the Mascot search engine against the complete UniProt proteome dataset (downloaded August 2019, 98,300 unique forward sequences) with a stringency of 0.1% FDR against a decoy database. The following parameters were used for peptide spectrum matching : trypsin (up to 2 missed cleavages), precursor mass tolerance of 7 ppm, 500 mmu fragment ion mass tolerance, phosphorylation as a variable modification (S/T/Y + 79.9963 Da), oxidation as a variable modification (M +15.9949), and both SILAC labelling (K: +8.0142 Da, R: +10.0083 Da) for the analysis of CAR-T cells and carbamamidomethylation (C +57.0215) as a static modification . Relative peptide abundance was determined using peak area integration and retention time alignment of selected ion chromatograms. The abundance of pY peptides was normalised using the spike in standard peptide LIEDpYTAK, and any samples without LIEDpYTAK sequenced were omitted. Statistical significance between the log2 mean abundance for each comparison was determined using Welch’s T test and corrected using the method of Storey(Storey and Tibshirani 2003) as previously described. Post translational modification signature enrichment analysis was performed as previously described(Krug et al. 2019).ProteomicsArthur SalomonBrown University, MCB DepartmentPARTIALHomo Sapiens (human)art@drsalomon.com10.1038/S41598-026-47234-XBrown UniversityUnited StatesfalsePhosphotyrosine proteomics reveals novel Zap70 and Itk pathway targets downstream of TCR and CAR in Jurkat T cellsζ-associated protein of 70 kDa (Zap70) and interleukin-2-inducible T cell kinase (Itk) propagate the primary and CD28-integrated phosphotyrosine (pY) signalling, respectively, to achieve full T cell activation. Despite their canonical roles in T cell activation, our understanding of how each kinase controls canonical and noncanonical pY signalling is incomplete. Here, using three T cell activation methods (soluble antibodies, APC-pMHC/TCR, and CD19-CAR/Raji), we evaluated the effects of two novel inhibitors, RDN2150 (RDN, Zap70) and Soquelitinib (Soq, Itk), on T cell activation. We validated the published working concentrations of RDN and Soq on phosphorylation of key T cell signalling proteins and on T cell activation markers, finding that RDN provides more complete inhibition of T cell signalling and activation. We used LC-MS/MS to evaluate how RDN and Soq treatment affected the phosphotyrosine (pY) signalling and proteome of T cells, finding that RDN, as opposed to Soq, completely downregulated the TCR signalling pathway. Finally, we identified new, noncanonical pY sites responsive to RDN and Soq, providing new insights into the pathways regulated by Zap70 and Itk. Together, our work provides a basis for further study on RDN and Soq, as well as a molecular roadmap for the effects of these inhibitors. 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