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2-A02-NoB2M_inj2_bio2_DIAHiSe_50min_GA5_1_4906.d.zipprimaryOK200henning.urlaub@mpinat.mpg.deYehor HorokhovskyiMass SpectrometryData-independent acquisitionAcute LeukemiaLymphomaHla-iLc-msmsImmunopeptidomeMhc-ihttps://www.ebi.ac.uk/pride/archive/projects/PXD063813Permanent Cell Line CellBloodThe cells were pelleted in 15 mL Falcon tubes and 200 µL of 4% sodium dodecyl sulfate (SDS) in 50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) supplied with Halt Protease Inhibitor Cocktail (Thermo Scientific) buffer was added to each of the cell pellets. Lysis buffer was carefully pipetted several times, followed by incubation at room temperature for 10 min. The samples were subsequently sonicated using a Bioruptor pico (Diagenode) for 40 min at maximum power using 30 s on and 30 s off cycles. As there was still residual DNA, 1 µL of benzonase (Thermo Scientific Pierce) was added to each sample and incubated at 37 °C for 30 min. The samples were subjected to another 20 min of sonication in Bioruptor using the settings described above and no residual DNA was left. Debris was pelleted by centrifuging the samples at 14,000g for 15 min and supernatant was transferred to 1.5 mL Eppendorf tubes. Protein concentration was determined by BCA assay (Thermo Scientific) and 100 µg protein per sample were used for further sample preparation. 10 mM Bond-Breaker TCEP (Thermo Scientific) and 20 mM iodoacetamide (IAA, Thermo Scientific) were added to each sample and incubated for 30 min at 37 °C. Sample clean-up was then performed according to an adapted version of the sp3 protocol (Hughes, Moggridge et al. 2019). In short samples were added to a 1:1 mixture of Sera-Mag SpeedBeads Carboxyl Magnetic Beads (hydrophobic and hydrophilic, Cytiva) with a protein to bead ratio of 1:10, which was pre-washed two times with water. Pure ACN was added to the lysate-bead-mixture until a final ACN concentration of 70% was reached. The samples were sonicated for 2 min in a water bath sonicator and incubated at room temperature, 950 rpm for 10 min in a thermomixer. Eppis were rested on a magnet rack for 2 min and the supernatant was removed. The samples were then washed three times with 90% ACN using the magnetic rack and supernatants were discarded after each washing step. Eppis were left open to dry for 5 min, beads were then carefully resuspended in 200 µL 25 mM TEAB and samples were sonicated for 2 min in water bath sonicator. Sequencing grade trypsin (Promega) was added in an enzyme:protein ratio of 1:50 and samples were incubated at 37 °C, 950 rpm for 16 h. Samples were briefly spun down after incubation, placed on the magnetic rack for 2 min and the supernatant was transferred to fresh Eppendorf tubes. Another 50 µL of 25 mM TEAB was added to the beads and after brief incubation on the magnet the supernatant was combined with the previous. The samples were then acidified to pH < 2 using TFA and desalted using C18 MicroSpin columns (Harvard Apparatus). Columns were preconditioned once with 100% ACN and equilibrated twice using 0.1% TFA. Samples were then loaded twice and washed three times using 0.1% TFA. They were then sequentially eluted using 40, 50 and 60% ACN in 0.1% TFA. Sequential eluates for each sample were combined and dried in a vacuum centrifuge (Eppendorf). For MS analysis, samples were resuspended in 5% ACN/0.1% FA and transferred into sample vials. LC-MS analysis was performed on a timsTOF Pro 2 mass spectrometer (Bruker Daltonics) coupled to a Dionex UltiMate 3000 nanoLC system (Thermo Scientific) with two injection replicates using a sample volume equivalent to 250 ng each per sample. The peptides were separated on an Aurora CSI C18 column (25 cm x 75 µm, 1.6 µm, IonOptics) at a constant temperature of 50 °C, using a trap column setup (PEPMAP100 C18, 0.3 x 5 mm, 5 µm, Thermo, # 160454). Buffer A consisted of 0.1% (v) formic acid in water and buffer B of 80% (v) ACN and 0.08% (v) formic acid. The gradient was set as follows, with linear changes to flow and % buffer B: 0-3.5 min 0.4 µL/min 5% (v) buffer B, 3.5-5 min 0.4-0.2 µL/min 5-10% B, 5-40 min 0.2 µL/min 10-46% B, 40-41 min 0.2 µL/min 46-95% B, 41-45 min 0.2 µL/min 95% B, 45-45.5 min 0.2-0.4 µL/min 95-5% B, 45.5-50 min 0.4 µL/min 5% B. Nano electrospray (Bruker CaptiveSpray) was used in positive ionization mode with a capillary voltage of 1.5 kV and dry gas flow rate of 3 L/min at a temperature of 180 °C. TIMS chamber was filled with nitrogen at 305 K temperature. Tunnel entrance pressure was 2.7 mbar. Data was recorded in high-sensitivity data-independent acquisition (DIA) PASEF mode, using the following settings: an ion mobility range of 1/K0 1.43 to 0.6 Vs/cm2 using equal ion accumulation and ramp times in the dual TIMS analyzer of 100 ms each was sampled. Collision energy was adjusted as a function of ion mobility: 59 eV at 1/K0 1.43 Vs/cm2 to 20 eV at 1/K0 0.6 Vs/cm2. In total, 16 PASEF scans were performed with two mass windows per scan.PrideDIA-NN (version 2.0.0) was used for the analysis of the MS data. First, an in-silico library was generated using the options “Reannotate”, “Contaminants”, “FASTA digest for library-free search/library generation” and “Deep learning-based spectra, RTs and IMs prediction”. The spectral library was generated from a FASTA file containing the UniProt human reference proteome (20645 entries, downloaded April 2024) and a translation sequence of B2M-HLA construct. The following settings were used: Trypsin/P with maximum 2 missed cleavages; protein N-terminal M excision; Carbamidomethyl(C) as fixed modification; Ox(M) and Ac(N-term) as variable modifications; peptide length from 7 to 30; precursor charge 1–4; precursor m/z range from 300 to 1800; fragment m/z range from 200 to 1800. In a next step the raw files were loaded into DIA-NN and searched using the “Unrelated Runs” function to calculate the optimized MS1 and MS2 mass accuracies for each raw file. These were then fixed to 10 ppm for MS1 and 15 ppm for MS2 for the main search, which was performed using the following settings: FDR 1%; scan window set to 0; MBR turned on; protein inference at gene level; scoring set to “Peptidoforms”; machine learning set to “NNs (cross-validated)”; quantification strategy set to QuantUMS (high precision) and cross-run normalization set to “RT-dependent”.ProteomicsHenning UrlaubPARTIALBioanalytical Mass Spectrometry Group Max-Planck-Institute for Multidisciplinary Sciences Goettingen, GermanyHomo Sapiens (human)42204932 Barajas Molina A, Horokhovskyi Y, Acuti N, Chong YK, Phanichkrivalkosil M, Siddons S, Afrache H, Maloney M, Soh WT, Hofland T, Hall C, Urlaub H, Kassiotis G, Liepe J, Mishto M. Stable β2-Microglobulin-HLA Class I Association Reshapes the Antigenic Landscape and TCR Recognition of Cancer-Associated Epitopes. Eur J Immunol. 2026 56(5):e70210 10.1002/eji.70210yehor.horokhovskyi@mpinat.mpg.deMax-Planck-Institute for Multidisciplinary SciencesGermanyβ2-Microglobulin (β2m) is essential for the stability and surface expression of human leukocyte antigen class I (HLA-I) molecules. While β2m's structural role is well established, its influence on the antigenic landscape remains incompletely understood. Here, we investigated how constitutive β2m binding to HLA-I influences the antigenic landscape in the context of cancer-associated epitopes. Using two engineered cell lines expressing β2m fused to the HLA-I heavy chain, we analysed changes in immunopeptidomes and epitope presentation. Despite cell line-specific transcriptional responses, the fusion of β2m to HLA-I consistently reduced peptide editing and resulted in convergent remodelling of the antigen presentation pathway (APP). The fusion further altered peptide selection, favouring the display of lower-affinity peptides derived from endogenous proteins while impairing high-affinity peptide presentation on HLA-I molecules. These changes were not attributable to APP component abundance but rather reflected mechanistic alterations in peptide selection and impacted T cell receptor recognition of tumour epitopes. Our findings suggest that β2m-HLA-I fusion can distort the physiological antigenic repertoire and T cell recognition, with implications for epitope discovery, immunotherapy design, and studies of HLA-I-mediated immune surveillance.Stable β2-Microglobulin-HLA Class I Association Reshapes the Antigenic Landscape and TCR Recognition of Cancer-Associated Epitopes.Barajas Molina Ana A, Horokhovskyi Yehor Y, Acuti Nicole N, Chong Yee Kien YK, Phanichkrivalkosil Meghna M, Siddons Sophie S, Afrache Hassnae H, Maloney Megan M, Soh Wai Tuck WT, Hofland Tom T, Hall Callum C, Urlaub Henning H, Kassiotis George G, Liepe Juliane J, Mishto Michele MfalseThe covalent bonding of beta-2-microglobulin with HLA class I influences the antigenic landscape of cellsHere, we investigate the effect that a constant interaction of beta-2m with HLA-I molecules can have on what antigens and peptides are displayed upon direct- and cross-presentation. When beta-2m is linked to HLA-I molecules the antigenic landscape is modified compared to physiological conditions.2026-06-042025-05-09PXD063813NEWT:6945NEWT:184922NEWT:6703NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2102NEWT:2042546NEWT:259447NEWT:45351NEWT:43179NEWT:4513NEWT:180454NEWT:5722NEWT:1247NEWT:1129NEWT:376741NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:281395NEWT:10360NEWT:1211601NEWT:876138NEWT:47664NEWT:317548NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:82688NEWT:95648NEWT:3885NEWT:3888NEWT:5821NEWT:1589NEWT:135622NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:28909NEWT:515849NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:913645NEWT:1000589NEWT:85963NEWT:85962NEWT:143361NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4442NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:44586NEWT:626528NEWT:3347NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:294381NEWT:197NEWT:1390363NEWT:77133NEWT:288705NEWT:29176NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:556182NEWT:1270NEWT:374990NEWT:1392NEWT:498217NEWT:156471NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:156476NEWT:286NEWT:391619NEWT:360104NEWT:287NEWT:246197NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:5508NEWT:294128NEWT:11676NEWT:55571NEWT:35500NEWT:1140NEWT:100226NEWT:4530NEWT:1143NEWT:4896NEWT:75058NEWT:13616NEWT:1390NEWT:1094343NEWT:1336795NEWT:172NEWT:296543NEWT:316435NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:82380NEWT:105023NEWT:866628NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:375146NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NEWT:8175NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:47946NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:243277NEWT:990119NEWT:2850NEWT:408172NEWT:227321NEWT:408170NEWT:493760NEWT:106590NEWT:260710NEWT:257313NEWT:3827NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:46704NEWT:1436733NEWT:460519NEWT:1187947NEWT:572307NEWT:1432138NEWT:269796NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:54571NEWT:9598NEWT:8030NEWT:9483NCBITaxon:40559NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:759272NEWT:432359NEWT:46835NEWT:1182263NEWT:109757NEWT:943146NEWT:2711NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:9103NEWT:1883446NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:3635NEWT:5811NEWT:235443NEWT:180923NEWT:108458NEWT:272623NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:118499NEWT:169963NEWT:32644NEWT:527796NEWT:225117NEWT:746128NEWT:499175NEWT:109779NEWT:43665NEWT:1266464NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:649908NEWT:410289NEWT:373153NEWT:375451NEWT:352472NEWT:357NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:411469NEWT:84023NEWT:559292NEWT:39491NCBITaxon:5811NEWT:29491NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:1328426NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NEWT:40483NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:38293NEWT:1428NEWT:327159NEWT:178876NEWT:1660NEWT:327160NEWT:573NEWT:9031NEWT:1872122NEWT:7091NEWT:108931NEWT:241368NEWT:1055524NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:7237NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:187878NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1821314NEWT:1249668NEWT:7108NEWT:317NEWT:5286NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:9644NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:554NEWT:27592NEWT:98334NEWT:426428NEWT:451516NEWT:63459NEWT:1276815NEWT:36185NEWT:588858NEWT:9639NCBITaxon:11071NEWT:242231NEWT:7574NEWT:1715256NEWT:7215NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:2172103NEWT:6494NEWT:7460NEWT:6491NEWT:507601NEWT:643680NCBITaxon:6157NEWT:42752NEWT:746360NEWT:6239NEWT:470150NEWT:162425NEWT:216257NEWT:102169NEWT:543734NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:118503NEWT:115357NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NEWT:13164NEWT:216129NCBITaxon:2NEWT:985076NEWT:1215323NEWT:2664179NEWT:986NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:1194669NEWT:51329NEWT:40559NEWT:243230NEWT:8355NEWT:633NEWT:9685NEWT:7029NEWT:1080772NEWT:8479NEWT:1283300NEWT:632NEWT:6183NEWT:6063NEWT:630NEWT:49240NEWT:334747NEWT:61235NEWT:15368NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:469008NEWT:260707NEWT:256318NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:1719NEWT:703612NEWT:260705NEWT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