{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/902-10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/908-10C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/902-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/908-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/4-1B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/901-10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/4-10B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/908-1B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/902-1B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/901-1B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/892-10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/892-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/892-10C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/4-10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/892-1C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/901-10C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/902-1C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/4-1C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/901-1C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/901-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/908-1C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/892-1B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/902-10B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/892-10B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/901-10B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/4-10C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/908-10B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/902-10C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/4-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/908-10.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069336/Analysis.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["nir.london@weizmann.ac.il"],"submitter":["Ronen Gabizon"],"technology_type":["Mass Spectrometry","Data-independent acquisition"],"software":[""],"submitter_keywords":["Alkyne probe","Btk","Ibrutinib"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD069336"],"tissue":["B Cell","Blood"],"sample_protocol":["Mino cells were grown in RPMI medium + 15% FBS and harvested. The cells were lysed by resuspension in ice - cold Mg / Ca free phosphate buffered saline, supplemented with protease inhibitors (Sigma P8340). The samples were sonicated by probe (22% amplitude, 16 pulses of 2 seconds), followed by centrifugation (21000×g at 4°C). The protein concentration was estimated using BCA, and the lysate was diluted to 2 mg/ml in PBS. Molecules (or DMSO) were added to a concentration of 1 µM or 10 µM, and incubated with the lysates for 1 hour at room temperature. At this point to each sample (250 µl) was added 0.75 µl of 50 mM biotin azide, 12.5 µl CuSO4:THPTA 20 mM:100 mM and 10 µl of 200 mM freshly dissolved sodium ascorbate. The samples were incubated at room temperature in the dark for 1.5 hours and precipitated with methanol chloroform. The pellets were dissolved in 250 µl 2.5% SDS in PBS using sonication (22%, 10 pulses of 2 seconds), diluted to 5 ml with PBS, then added PBS washed SA beads from Cytiva (10 µl beads each sample). Beads were tumbled in the  solution for 3 hours at 25°C, then washed as follows: 3 washes with 0.4 ml of 1% SDS/PBS; resuspension in 0.3 ml 1% SDS/PBS, addition of 3 µl 1 M DTT, followed by 45 min incubation at 25°C; addition of 25 µl of 0.8 M iodoacetamide (freshly dissolved in water), followed by 40 minutes incubation at 25°C; 3 washes with 0.6 ml of 6 M Urea (freshly dissolved) in PBS; 5 washes with 0.6 ml of 20% methanol in PBS; 1 wash with 0.6 ml of PBS; two washes with 0.6 ml water.  The beads were then transferred to new tubes using two portions of 100 µl 50 mM triethylammonium bicarbonate (TEAB), and 2 µg of trypsin (Promega) were added to each sample. The samples were shaken overnight at 37°C. Following the digestion, the beads were centrifuged and the supernatant was transferred to a new tube. The beads were further washed with 50 mM TEAB + 2 M NaCl, and the wash was combined with the first supernatant. The samples were mixed with 40 µl of 1% TFA in water, and desalted using Oasis desalting columns (Waters) as per the manufacturer’s instructions. The eluted samples were evaporated and dissolved in 40 µl of 3% acetonitrile in water + 0.1% formic acid. 1.5 µl were injected per sample. 3 samples were injected per condition. Samples were analysed using EASY-nLC 1200 nano-flow UPLC system, using PepMap RSLC C18 column (2 μm particle size, 100 Å pore size, 75 μm diameter × 50 cm length), mounted using an EASY-Spray source onto an Exploris 240 mass spectrometer. uLC/MS-grade solvents were used for all chromatographic steps at 300 nL/min. The mobile phase was: (A) H2O + 0.1% formic acid and (B) 80% acetonitrile + 0.1% formic acid. Peptides were eluted from the column into the mass spectrometer using the following gradient: 1–40% B in 160 min, 40–100% B in 5 min, maintained at 100% for 20 min, 100 to 1% in 10 min, and finally 1% for 5 min. Ionization was achieved using a 1800 V spray voltage with an ion transfer tube temperature of 275 °C. Data were acquired in data independent acquisition (DIA) using the same gradient described. Ionization was achieved using a 1800 V spray voltage with an ion transfer tube temperature of 275 °C. MS1 resolution was set to 60,000 (at 200 m/z), a mass range of 375–1650 m/z, normalized AGC of 300%, and the maximum injection time was set to 20 ms. DIA was measured with a precursor mass range of 390-920, 17 isolation windows, orbitrap resolution of 30,000 at 200 m/z, maximum injection time of 50 ms and HCD collision energy of 27%."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Fragpipe was used to analyze the data with quantification by DIA-NN (version 1.8.2 beta), with carbamidomethyl as a fixed modification, and methionine oxidation and N-terminal acetylation as variable modifications."],"omics_type":["Proteomics"],"labhead":["Nir London"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel"],"species":["Homo Sapiens (human)"],"publication":["42151150 Petri L, Gabizon R, Péczka N, Ábrányi-Balogh P, Simon J, Imre T, Ferenczy GG, London N, Keserű GM. α-Halothioamide warheads with enhanced cysteine reactivity and specificity for covalent protein labelling. Nat Commun. 2026 17(1):6824 10.1038/s41467-026-72993-6"],"submitter_mail":["ronen.gabizon@weizmann.ac.il"],"submitter_affiliation":["Department of Chemical and Structural Biology, Weizmann Institute of Science"],"submitter_country":["Israel"],"pubmed_abstract":["Covalent labelling is a promising modality relying on electrophilic warheads that form covalent bonds with their targets. Here we present the oxygen-to-sulfur exchange strategy, that transforms traditional carboxamides to thioamides, yielding electrophilic warheads, including chlorothioacetamides and fluorothioacetamides, with enhanced cysteine reactivity, while retaining aqueous stability and selectivity. We demonstrate their utility in targeted covalent inhibitor development targeting Janus kinase 3 and Bruton's tyrosin kinase, when installed on relevant scaffolds and also in the development of antibody-drug conjugates. Next, alkyne-tagged α-halothioamide probes are evaluated by quantitative chemoproteomics. These studies reveal that the chlorothioacetamide probe preferentially labelled a distinct subset of the proteome, which results in Cys-targeted covalent phosphodiesterase 6δ labelling with functional impact. We discuss that the oxygen-to-sulfur exchange strategy offers alternative cysteine-specific thioamide-derived warheads and enables precise and even late-stage modulation of covalent reactivity, highlighting their promise for covalent probe design and applications in medicinal chemistry and chemical biology."],"pubmed_title":["α-Halothioamide warheads with enhanced cysteine reactivity and specificity for covalent protein labelling."],"pubmed_authors":["Petri László L, Gabizon Ronen R, Péczka Nikolett N, Ábrányi-Balogh Péter P, Simon József J, Imre Tímea T, Ferenczy György G GG, London Nir N, Keserű György M GM"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic selectivity of BTK-targetting probes derivatizes with thiohaloacetamide warheads","description":"Mino cell lysates were incubated with alkyne-modified probes derived from ibrutinib, containing either acrylamide, chloro/fluoro acetamide or thiochloro/thiofluoro acetamide warheads. The reacted proteins were enriched and quantified using 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