Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/Pride_excel_doc.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240722_Ramos_20uM_2h_MB-15A-15B-16A-16B_10uM_1h_MB-13A-13B-14A-14B_rep1.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240722_Ramos_20uM_2h_MB-15A-15B-16A-16B_10uM_1h_MB-13A-13B-14A-14B_rep2.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240517_Ramos_50uM_2h_MB-15A-15B-16A-16B_10uM_1h_MB-13A-13B-14A-14B_rep2.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240516_Ramos_50uM_2h_MB-15A-15B-16A-16B_10uM_1h_MB-13A-13B-14A-14B_rep1.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-260_09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240510_has-ii-259_07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-271_07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055926/20240717_has-ii-270_02.rawprimaryOK200cravatt@scripps.eduHayden SharmaMass SpectrometryBottom-up proteomicsNot availableChemical biologyProteomicsChemical synthesisCovalent probeshttps://www.ebi.ac.uk/pride/archive/projects/PXD055926Cell Suspension CultureLymphocyte Of B LineageRamos cells (suspension cells: 8 ml at 3 million cells ml−1; seeded 1 h before treatment) were treated with DMSO or 20 μM non-alkyne competitor stereoprobes for 2 h. The cells were further treated with 10 μM stereochemically matched alkyne probes for 1 h, then the cells were washed three times with chilled DPBS, and immediately processed or stored at −80 °C. The cell pellets were resuspended in 500 μl of cold DPBS and lysed by sonication (2 × 15 pulses, 10% power output). The total protein content of the whole-cell lysates was measured using a Pierce BCA protein assay kit. The samples were normalized to 2 mg ml−1 and 500 μl (1 mg of proteome) treated with 55 μl of click mix (30 μl of 1.7 mM TBTA in 4:1 t-BuOH:DMSO, 10 μl of 50 mM CuSO4 in H2O, 5 μl of 10 mM biotin-PEG4-azide in DMSO, 10 μl of freshly prepared 50 mM tris(2-carboxyethyl)phosphine in DPBS) for 1 h at r.t. with vigorous vortexing every 20 min. Proteins were precipitated out of solution by the addition of chilled HPLC-grade methanol (600 μl), chloroform (200 μl) and water (100 μl), followed by vigorous vortexing and centrifugation at 16,000g for 10 min, to create a disk. Without disrupting the protein disk, both top and bottom layers were aspirated, and the protein disk re-sonicated in 500 μl of methanol and centrifuged at 16,000g for 10 min. After complete aspiration of the methanol, protein pellets were frozen at −80 °C or immediately resuspended in 500 μl of freshly made 8 M urea in DPBS, followed by the addition of 10 μl of 10% SDS, and pellet was sonicated to clarity. The samples were reduced with 25 μl of 200 mM dithiothreitol (DTT) at 65 °C for 15 min, followed by alkylation with 25 μl of 400 mM iodoacetamide at 37 °C for 30 min. The samples were quenched with 130 μl of 10% SDS, transferred to a 15-ml tube, and the total volume was brought to 6 ml with DPBS (0.2% final SDS). Washed streptavidin beads (Thermo, catalogue number 20353; 100 μl of 50% slurry/ sample) was then added and the probed labelled protein enriched for 1.5 h at r.t. with rotation. After incubation, the beads were pelleted (2 min × 2,000g) and washed with 0.2% SDS in DPBS (2 × 10 ml), DPBS (1 × 5 ml, then transferred to a protein low-bind Eppendorf safe-lock tube), high-performance liquid chromatography (HPLC) water (2 × 1 ml) and 200 mM 4-(2-hydroxyethyl)-1-piperazinepropanesulfonic acid (EPPS; 1 × 1 ml) at r.t. Enriched proteins were digested on-bead overnight with 200 μl of trypsin mix (2 M urea, 1 mM CaCl2, 10 μg ml−1 trypsin, 200 mM EPPS, pH 8.0). The beads were spun down, supernatant was collected and 100 μl of acetonitrile (30% final) was added, followed by 6 μl of 20 mg ml−1 (in dry acetonitrile) of the corresponding TMT16plex tag (for competitive protein-directed ABPP or TMT10plex for non-competitive protein-directed ABPP) for 1.5 h at r.t. with vortexing every 30 min. TMT labelling was quenched by the addition of hydroxylamine (6 μl 5% solution in H2O) and incubated for 15 min at r.t. Samples were then acidified with 20 μl 100% formic acid, combined and dried with a SpeedVac. Samples were desalted with a Sep-Pak column and then high pH fractionated into ten fractions using peptide desalting spin columns.PrideEnrichment ratios (probe versus probe) were calculated for each peptide–spectra match by dividing each TMT reporter ion intensity by the sum intensity for all the channels. Peptide–spectra matches were then grouped based on protein ID and (excluding peptides with summed reporter ion intensities <10,000) coefficient of variation of >0.5, and <2 distinct peptides. Replicate channels were grouped across each experiment, and average values were computed for each protein. A variability metric was also computed across replicate channels, which equaled the ratio of the median absolute deviation to the average for channels corresponding to the highest enriching probe and was expressed as a percentage. A protein was considered stereoselectively enriched if the variability corresponding to the alkyne probe leading to highest enrichment did not exceed 20% and the average enrichment by the alkyne probe was greater than threefold that of its enantiomer. A protein was considered stereoselectively liganded if enantioselective enrichment was greater than twofold the enrichment observed following treatment with a stereochemically matched non-alkyne competitor. For comparison to the MY series, a protein was considered stereoselectively enriched in a chemotype-selective manner if it was enantioselectively enriched >3-fold by a stereoprobe from one chemotype and <2-fold by the highest enriching stereoprobe from the other chemotype. Conversely, a protein was considered a shared stereoselective target if it was enantioselectively enriched >3-fold by a stereoprobe from one chemotype and >2-fold by a stereoprobe from the other chemotype. For liganding comparison, a protein was considered stereoselectively liganded in a chemotype-selective manner if it was enantioselectively enriched >3-fold by a stereoprobe with >50% competition from the stereomatched competition from one chemotype and enriched with <2-fold enantioselectivity or >30% competition by the other chemotype. Conversely, a protein was considered a chemotype-selective liganded target if it was enantioselectively enriched >3-fold by a stereoprobe with >50% competition from the stereomatched competition from one chemotype and enantioselectively enriched <2-fold or with <30% competition by a stereoprobe from the other chemotype.ProteomicsDr. Benjamin F. CravattDepartment of Chemistry, The Scripps Research Institute, La Jolla, CA, USA (lab head)PARTIALHomo Sapiens (human)40501015 Bielecki M, Nassir M, Sharma HA, Truax NJ, Raheja N, Thompson TM, El-Hayek Ewing T, Melillo B, Cravatt BF, Baran PS. Enantiocontrolled Azetidine Library Synthesis via Strain-Release Functionalization of 1-Azabicyclobutanes. J Am Chem Soc. 2025 147(25):22209-22218 10.1021/jacs.5c07227hsharma@scripps.eduScripps ResearchUnited StatesA simple, modular, and programmable approach to access complex stereopure azetidines through strain-release functionalization is disclosed. The synthetic methods developed enable the parallel synthesis of stereodefined azetidines that would be otherwise laborious to produce. Given the privileged nature of these structures, a set of stereoprobes for use in activity-based protein profiling was prepared and evaluated, revealing proteins in human cancer cells, which were liganded with clear stereo- and chemo-selectivity.Enantiocontrolled Azetidine Library Synthesis via Strain-Release Functionalization of 1-Azabicyclobutanes.Bielecki Michael M, Nassir Molhm M, Sharma Hayden A HA, Truax Nathanyal J NJ, Raheja Nicholas N, Thompson Ty M TM, El-Hayek Ewing Tamara T, Melillo Bruno B, Cravatt Benjamin F BF, Baran Phil S PSfalseSimple , Enantiocontrolled Azetidine Library Synthesis via Strain-Release Functionalization of 1-AzabicyclobutanesHerein we describe a new enantioselective route for the synthesis of all stereoisomers of 2,3-disubstituted azetidines. This approach uses simple strain release functionalization of preformed 1-azabicyclobutanes (ABBs), which enables installation of a wide array of nucleophiles at the C3-position. Chemical proteomic profiling of stereoisomeric sets of cysteine-reactive acrylamides derived from the new azetidine library reveals ligandable protein sites distinct from those of azetidine probes synthesized using C–H arylation.2026-06-292024-09-17PXD055926NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:931281NEWT:4432NEWT:5762NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:1367269NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1436733NEWT:460519NEWT:1247411NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:84588NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:644223NEWT:235443NEWT:108458NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:215402NCBITaxon:548681NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:1034015NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:985076NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:28532NEWT:353152NEWT:8496NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:104395NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:74649NEWT:52638NEWT:57075NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:5322NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:553470NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:231490NEWT:7725NEWT:430615NEWT:563041NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1416333NEWT:35024NEWT:135461NEWT:1678078NEWT:749906NEWT:418985NEWT:1817808NEWT:749907NEWT:145263NEWT:69014NEWT:142809NEWT:694569NEWT:27606NEWT:9739NEWT:59202NEWT:9975NEWT:8643NEWT:51953NEWT:3197NEWT:860688NEWT:13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