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Barletta SolariMass SpectrometryBottom-up proteomicsKeywords: multiple sclerosis (ms)Immunoglobulin repertoireEpstein-barr virus (ebv)Immunoglobulin proteomeDisease modifying drugs (dmds)B cellshttps://www.ebi.ac.uk/pride/archive/projects/PXD075641Blood SerumPeripheral blood collection Peripheral blood (7.5 mL for serum) was collected from all patients. Serum was processed by centrifugation for 10 minutes at 3000 rpm and stored at -80 °C for till Ig purification process. Ig purification from serum and mass spectrometry of Ig peptides Serum samples from the OZA, DMF and TER patient cohorts were analyzed on Ig peptides. Ig enrichment was conducted in Pierce spin columns by using CaptureSelect LambdaXP and KappaXP affinity beads (Thermo Fisher Scientific, manufacturer’s instructions). Ig’s were collected in glycine buffer (0.1 M; pH 2 – 3) and stored at -80 °C. The protein concentration was determined via Bradford assay. For protein collection, the methanol / chloroform precipitation method was applied. Similar amount of total proteins was used per sample for the in-solution digest with trypsin. Resulting Ig peptides were analyzed with liquid chromatography tandem mass spectrometry (LC-MS/MS) on a linear trap quadrupole (LTQ) Orbitrap Velos mass spectrometer (Thermo Fisher Scientific). Detailed methodology is described elsewhere. Samples were measured in data-dependent acquisition (DDA) mode in case of DMF and TER, and the OZA data set was measured in optimized data-independent acquisition (DIA) mode at a later stage due to method availability. We performed Ig extraction prior to mass spectrometry and consistently applied the same method for the longitudinal analysis of each patient subgroup to avoid bias from using these two slightly different methods.PrideNot availableThe raw mass spectra data was analyzed using the workflow nf-core/quantms (version 1.0) selecting Comet and Percolator for DDA- and DIA-NN for DIA-based library free peptide database search. A stringent peptide-level FDR cut-off of 0.1 for DDA and 0.01 for DIA was set. Patient-specific Ig sequence databases for the peptide search were generated from the translated AA sequence of the corresponding Ig transcriptomic data, thereby combining the BL and FUP6 sequences to one database for a more sensitive peptide identification. Data was analyzed as described previously. Downstream analyses were performed with in-house R scripts that were adapted individually for each data set with considering the DIA and DDA modes (https://github.com/qbic-projects/MS-treatment-study). Ig sequences were considered a match if covered by unique peptides with ≥ 30% identity to the somatically mutated CDR3 cDNA sequence of the VH sequence. For the transcriptome-proteome alignments, transcriptome BCR sequences were considered across the repertoires before and after treatment to match with the proteome samples.ProteomicsFrancesca Barletta SolariQuantitative Biology Center (QBiC), University of Tübingen, Germany.PARTIALHomo Sapiens (human)francesca.barletta-solari@qbic.uni-tuebingen.de41981407 Vasilenko N, Ruschil C, Stadelmaier J, Tieck MP, Schembecker S, Owens GP, Bennett JL, Berthele A, Ziemann U, Poli S, Snaidero N, Nahnsen S, Jarboui MA, Bichmann L, Gabernet G, Kowarik MC. Extensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugs. J Neuroinflammation. 2026 23(1):128 10.1186/s12974-026-03735-01. Quantitative Biology Center (QBiC), University of Tübingen, Germany 2. M3 Research Center, University Hospital Tübingen, GermanyGermanyExtensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugs.Vasilenko Nicole N, Ruschil Christoph C, Stadelmaier Josua J, Tieck Maria P MP, Schembecker Sonja S, Owens Gregory P GP, Bennett Jeffrey L JL, Berthele Achim A, Ziemann Ulf U, Poli Sven S, Snaidero Nicolas N, Nahnsen Sven S, Jarboui Mohamed A MA, Bichmann Leon L, Gabernet Gisela G, Kowarik Markus C MCfalseExtensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugsB cells are crucial players in the pathogenesis of multiple sclerosis (MS), however, limited information is available on peripheral immunoglobulin (Ig) repertoires of people with MS (pwMS) in comparison to healthy individuals and during different treatments. Next generation sequencing of Ig heavy chains (VH) originating from bulk-sorted B cell populations was performed in 33 pwMS and ten healthy controls. All 33 pwMS were examined longitudinally at baseline and six months after treatment with ozanimod, fingolimod, dimethyl fumarate, teriflunomide, cladribine or natalizumab. Ig peptides were obtained longitudinally in a subset of treated pwMS by Ig mass spectrometry, overlapped with VH transcriptomes through nf-core bioinformatics workflow analysis and additionally Ig serum level and anti-Epstein-Barr virus IgG level (EBNA1) were measured. VH repertoires of treatment-naïve pwMS showed a significantly decreased diversity in the double negative B cells and different usage of IGHV genes when compared with healthy controls. Quantitative changes in B cell subsets during treatment were accompanied by qualitative changes in Ig repertoires with a significantly decreased diversity in the naive, memory B cells and plasmablasts during ozanimod treatment. A similar trend was noticeable for all other treatments except natalizumab. No qualitative change in Ig peptides overlapping with Ig transcriptome repertoires was observed. This study provides first evidence for an altered peripheral Ig repertoire in pwMS. In addition, various treatments seem to shift the composition of B cells towards an increased fraction and activation of the naive B cell pool and a reduced fraction of memory B cells with reduced clonal diversity.2026-04-272026-03-14PXD075641NEWT:1773NEWT:3555NEWT:1182590NEWT:10090NEWT:749200NEWT:35554NEWT:4120NEWT:5693NEWT:347515NEWT:1216979NEWT:307972NEWT:92867NEWT:990346NEWT:544496NEWT:5334NEWT:145953NEWT:284812NEWT:115104NEWT:43330NEWT:67825NEWT:44544NEWT:13076NEWT:544404NEWT:3702NEWT:8839NEWT:4232NEWT:1736309NEWT:4113NEWT:7227NEWT:11298NEWT:885318NEWT:4081NEWT:876138NEWT:554NEWT:5691NEWT:260710NEWT:106592NEWT:237561NEWT:9913NEWT:10036NEWT:4100NEWT:7574NEWT:1351NEWT:1076NEWT:6763NEWT:7215NEWT:380394NEWT:272563NEWT:1639NEWT:188229NCBITaxon:79857NEWT:746360NEWT:6239NEWT:135588NEWT:135622NEWT:6915NEWT:9986NEWT:101510NEWT:3880NEWT:58002NEWT:9103NEWT:4577NEWT:146479NEWT:1000589NEWT:145943NEWT:85962NEWT:160488NEWT:317447NEWT:3635NEWT:7955NCBITaxon:2NEWT:7959NEWT:2261NEWT:3197NEWT:9615NEWT:884019NEWT:4565NEWT:1264690NEWT:169963NCBITaxon:38727NEWT:36329NEWT:34305NEWT:59729NCBITaxon:183674NEWT:626528NEWT:139927NEWT:4558NEWT:9606NEWT:367830NEWT:243230NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NEWT:470NCBITaxon:79824NCBITaxon:4563NEWT:3218NEWT:5759NEWT:9838NCBITaxon:9615NEWT:1736231NEWT:1193501NEWT:6287NEWT:6326NEWT:9796NEWT:2762NEWT:5476NEWT:562NEWT:260707NEWT:287NEWT:10117NEWT:10116NEWT:1280NEWT:1836NEWT:29760NEWT:260705NEWT:1148NEWT:4932NEWT:70448NEWT:9825NEWT:3603NEWT:698936NEWT:39946NEWT:11676NEWT:9823NEWT:100226NCBITaxon:6073NEWT:4896NEWT:6279NEWT:7370NEWT:573NEWT:6282NEWT:7091419814070009-0002-1396-2252