{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/MS_Samples.xlsx"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_2.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_4.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_6.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_8.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_16_1_01_3751.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_18_1_01_3753.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_10_1_01_3763.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_8_1_01_3761.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_17.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_19.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_1_1_01_3766.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_4_1_01_3771.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_9_1_01_3762.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_1.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_5.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_3.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_10.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_9.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_6_1_01_3759.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_7.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_17_1_01_3755.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_19_1_01_3756.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_5_1_01_3772.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_3_1_01_3769.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_7_1_01_3760.d.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_16.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_18.xy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075514/sample_2_1_01_3767.d.rar"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["m.luzarowski@zmbh.uni-heidelberg.de"],"submitter":["Marcin Luzarowski"],"technology_type":["Mass Spectrometry","Top-down proteomics"],"software":["Not available"],"submitter_keywords":["Biological degraders","Lysosomal degradation","Tri-n-acetylgalactosamine","Targeted protein degradation","Sil-6r","Asgpr","Il-6"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075514"],"sample_protocol":["Binder 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."],"repository":["pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Mass 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)."],"omics_type":["Proteomics"],"labhead":["Marcin Luzarowski"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["m.luzarowski@zmbh.uni-heidelberg.de"],"submitter_affiliation":["University of Heidelberg"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Glycan-based Biological Degraders Targeting the Cytokine Immune Axis","description":"The 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.","dates":{"publication":"2026-03-17","submission":"2026-03-11"},"accession":"PXD075514","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:150475","NEWT:9417","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:876138","NEWT:4081","NEWT:554","NEWT:98334","NEWT:237561","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:8782","NEWT:1000589","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:28104","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:931281","NEWT:7029","NEWT:1283300","NEWT:334747","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:300641","NEWT:4784","NEWT:727","NEWT:9796","NEWT:725","NEWT:360106","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:29760","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:6282","NEWT:1134506","NEWT:575584","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:1182590","NEWT:8726","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:4120","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:373995","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:106592","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NEWT:1911079","NEWT:145943","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:1480154","NEWT:1274414","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:884019","NEWT:169963","NEWT:36329","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:1450511","NEWT:470","NEWT:84023","NEWT:9838","NCBITaxon:9615","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:1274432","NEWT:1274426","NEWT:1423","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:9940","NEWT:573","NEWT:9031","NEWT:1274420","NEWT:7091"]}}