Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/MS_Samples.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_2.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_4.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_6.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_8.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_16_1_01_3751.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_18_1_01_3753.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_10_1_01_3763.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_8_1_01_3761.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_17.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_19.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_1_1_01_3766.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_4_1_01_3771.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_9_1_01_3762.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_1.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_5.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_3.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_10.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_9.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_6_1_01_3759.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_7.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_17_1_01_3755.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_19_1_01_3756.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_5_1_01_3772.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_3_1_01_3769.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_7_1_01_3760.d.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_16.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_18.xyftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_2_1_01_3767.d.rarprimaryOK200m.luzarowski@zmbh.uni-heidelberg.deMarcin LuzarowskiMass SpectrometryTop-down proteomicsNot availableBiological degradersLysosomal degradationTri-n-acetylgalactosamineTargeted protein degradationSil-6rAsgprIl-6https://www.ebi.ac.uk/pride/archive/projects/PXD075514Binder molecules including siltuximab, tocilizumab, sIL-6R, and a VHH against IL-6 were modified via TGN conjugation to enable lysosomal targeting. Purified proteins (>1 mg/mL) were reacted with Tris-GalNAc-PEG5-sulfo-NHS Ester (Sussex Research, MV1000054, 5 mg/mL in DMSO) in 1× PBS. Molar ratios of 1:1, 1:5, 1:10, and 1:25 were selected based on the number of available lysine residues. Reactions were incubated overnight at room temperature under rotation and subsequently quenched with Tris/HCl (pH 9.0) to a final concentration of 10 mM. Excess reagent was removed by three rounds of centrifugal filtration using Amicon® Ultra units (Merck Millipore) with MWCOs of 30 kDa for antibody-based BioDegs and 10 kDa for sIL-6R and VHH constructs. Samples were washed three times with 300 µL of 1× PBS to remove unbound components and exchange the buffer. The intact masses of proteins were determined by electrospray ionization mass spectrometry (ESI-MS) using a quadrupole time-of-flight (QTOF) mass spectrometer (Maxis, Bruker Daltonics) following desalting via high-performance liquid chromatography (HPLC, Agilent Technologies). A total of 200 µL of protein sample at a concentration of 0.25 µM was loaded onto a reversed-phase trapping column (0.8 × 2 mm, Poros R1; Applied Biosystems). After washing for 3 minutes with 0.3% formic acid at a flow rate of 300 µL/min, proteins were eluted using a mobile phase consisting of 40% isopropanol, 5% acetonitrile, and 0.3% formic acid at a flow rate of 40 µL/min.prideNot availableMass spectra were acquired in positive ion mode over an m/z range of 500–4000 using full-scan acquisition. The spectra rate was set to 2 Hz, and rolling average smoothing was applied with a 2× setting. Mass spectra were deconvoluted using the MaxEnt algorithm implemented in Compass DataAnalysis 4.2 software (Bruker Daltonics).ProteomicsMarcin LuzarowskiPARTIALCore Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, GermanyHomo Sapiens (human)Not availablem.luzarowski@zmbh.uni-heidelberg.deUniversity of HeidelbergGermanyfalseGlycan-based Biological Degraders Targeting the Cytokine Immune AxisThe project investigates targeted degradation of IL-6 and sIL6-R using bispecific Biological Degraders (BioDegs) that enable receptor-mediated uptake via the asialoglycoprotein receptor (ASGPR). Various IL-6(R)–binding scaffolds were modified with triantennary N-acetylgalactosamine (TGN) to promote lysosomal targeting. Mass spectrometry was used to determine the glycan-to-protein ratio after modification of the different binders, providing analytical characterization of the conjugates and confirming successful generation of BioDeg constructs.2026-03-172026-03-11PXD075514NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:544496NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:67825NEWT:13076NEWT:1249668NEWT:317NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:876138NEWT:4081NEWT:554NEWT:98334NEWT:237561NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:746360NEWT:6239NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:8782NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:83332NEWT:29760NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:7370NEWT:6282NEWT:1134506NEWT:575584NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:10090NEWT:935293NEWT:749200NEWT:4120NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:373995NEWT:544404NEWT:3702NEWT:129249NEWT:8839NEWT:4232NEWT:990119NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:106592NEWT:9913NEWT:1432138NEWT:10312NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:10306NEWT:1911079NEWT:145943NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:9606NEWT:367830NEWT:157295NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:9940NEWT:573NEWT:9031NEWT:1274420NEWT:7091