Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/identification.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/Peroxiredoxin-6_5018-68.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/ELAV2_2173-25.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/PENK_9076-25.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/DHPR_11257-1.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/PKC-G_5476-66.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/MAG_20579-50.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/NPY_20590-13.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/GFP_3849-56.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075602/NPTXR_15511-37.raw.zipprimaryOK200xiaotang@illinois.eduXiaotang LuAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryMSENot availablePulldown msNeurosciencehttps://www.ebi.ac.uk/pride/archive/projects/PXD075602BrainSOMAmer reagents (40 pmol) containing a terminal photocleavable biotin were immobilized on streptavidin-coated beads and incubated with 50 pmol recombinant protein target for 3 hours at 28°C in 190 µL Selection Buffer containing 20 µM polyanionic competitor (Z-Block26). SOMAmer-protein complexes were then challenged with 10 mM dextran sulfate (m.w. 5,000) and washed 6 times with 190 µL Selection Buffer. Samples were irradiated with a UV Bench Lamp XX-15L (15 W, 365 nm; Analytik Jena) for 17 min at 25°C to release SOMAmer-protein complexes via the photocleavable linker. SOMAmer-protein complexes were digested with 1 nM trypsin in 8 M urea, 200 mM iodoacetamide, 200 mM dithiothreitol, and 25 mM ammonium bicarbonate. Peptide fragments were desalted using an OASIS Prime HLB plate (Waters, cat. #186008053), eluted with 70% acetonitrile, dried, and reconstituted in 15 µL of 2% acetonitrile/0.1% formic acid. UPLC was performed on a Waters ACQUITY M-Class UPLC. Analytes were separated on a nanoEase HSS T3 100 Å, 1.8 µm, 300 µm × 150 mm column (Waters, cat. #186009249) with a 5 µL injection volume and 5 µL/min flow rate. The gradient consisted of 3-27% buffer B (0.1% formic acid in acetonitrile) in buffer A (0.1% formic acid in H₂O) from 0-13 min, followed by 27-95% buffer B from 13-14 min. The trap column and LC were both maintained at 60°C.PrideNot availableMS spectral analysis was performed using an MSE method on a Waters Xevo G2-S QTof mass spectrometer. The peptides were ionized using a narrow-bore ESI probe in positive ionization mode. A mass range of 50–1200 m/z (continuum mode) was utilized with a scan rate of 0.5 s and low/high collision energies of 4 V and 15-40 V, respectively. The capillary voltage was set to 1 kV, and the cone voltage was 40 V, with a cone gas flow of 40 L/h and a desolvation gas flow of 400 L/h (400°C). The source temperature was maintained at 120°C. Results from LC-MS/MS were analyzed and compared against protein databases using ProteinLynx Global Server v3.0.3 (PLGS).ProteomicsXiaotang LuUniversity of Illinois Urbana-ChampaignPARTIALHomo Sapiens (human)Mus Musculus (mouse)xiaotang@illinois.edu10.1038/S41467-026-72180-7University of Illinois Urbana-ChampaignUnited StatesfalseProbing molecular diversity of brain cells with chemically modified aptamersWe developed a volumetric correlated light and electron microscopy (CLEM) approach that uses slow off-rate modified aptamers (SOMAmers) for fluorescence labeling of cells in ultrastructurally reconstructable electron micrographs. The small size of aptamers enables intracellular labeling in fixed brain tissue without detergent permeabilization, thereby preserving tissue ultrastructure and allowing high-resolution electron microscopy imaging and accurate cellular segmentation. This method enables labeling of a wide range of molecular biomarkers, providing a powerful strategy to integrate molecular information with volumetric electron microscopy datasets. As a result, it facilitates molecularly annotated ultrastructural studies of complex tissues, including investigations of neural circuits. To ensure that the aptamers used in this method bind specifically to their intended protein targets, we validated target binding using pull-down mass spectrometry. These results were further confirmed through complementary approaches including genetic correlation analyses, proximity extension assays, and comparisons with commercial antibody labeling.2026-04-172026-03-13PXD075602NEWT:1773NEWT:3555NEWT:38783NEWT:1182590NEWT:2NEWT:10090NEWT:935293NEWT:749200NEWT:35554NEWT:4120NEWT:5693NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:92867NEWT:990346NEWT:544496NEWT:5334NEWT:145953NEWT:257309NEWT:5180NEWT:284812NEWT:115104NCBITaxon:1313NEWT:1081927NEWT:43330NEWT:67825NEWT:44544NEWT:13076NEWT:373995NEWT:544404NEWT:3702NEWT:8839NEWT:4232NEWT:990119NEWT:1736309NEWT:4113NEWT:7227NEWT:11298NEWT:7469NEWT:885318NEWT:171101NEWT:4081NEWT:876138NEWT:554NEWT:5691NEWT:408170NEWT:260710NEWT:3708NEWT:106592NEWT:237561NEWT:9913NEWT:10036NEWT:4100NEWT:7574NEWT:1351NEWT:1076NEWT:6763NEWT:7215NEWT:803NEWT:8030NEWT:380394NEWT:272563NEWT:507601NEWT:1639NEWT:188229NEWT:4909NCBITaxon:79857NEWT:746360NEWT:6239NEWT:1589NEWT:135588NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:95486NEWT:3880NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:1911079NEWT:1000589NEWT:145943NEWT:1902NEWT:85962NEWT:160488NEWT:317447NEWT:3635NEWT:7955NCBITaxon:2NEWT:235443NEWT:985076NEWT:7959NEWT:2261NEWT:3197NEWT:9615NEWT:884019NEWT:4565NEWT:1264690NEWT:169963NCBITaxon:38727NEWT:36329NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:9606NEWT:367830NEWT:243230NEWT:931281NEWT:373153NEWT:7029NEWT:1283300NEWT:334747NEWT:470NCBITaxon:79824NCBITaxon:4563NEWT:3218NEWT:5759NEWT:9838NCBITaxon:9615NEWT:1736231NEWT:1193501NEWT:6287NEWT:2242NEWT:6326NEWT:9796NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:260707NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:29760NEWT:260705NEWT:80863NEWT:1148NEWT:4932NEWT:70448NEWT:9825NEWT:3603NEWT:698936NEWT:2759NEWT:39946NEWT:11676NEWT:9823NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:7370NEWT:573NEWT:6282NEWT:7091NEWT:11345060000-0002-8575-5394