Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/11/PXD043999/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/11/PXD043999/SHIHR_9062_HLAPEPTIDE_041922.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/11/PXD043999/SHIHR_9060_HLAPEPTIDE_041922.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/11/PXD043999/9062_results.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/11/PXD043999/9060_results.datprimaryOK200jarhowlee@tictx.orgJAR-HOW LEEMass SpectrometryShotgun proteomicsNot availableHumanHla class iiMhc peptidomeDqhttps://www.ebi.ac.uk/pride/archive/projects/PXD043999B CellCell CultureSamples were loaded on 1ml C18 packed columns. Wash with 20ml 0.1% TFA. Elute with 2ml 50%ACN in 0.1% TFA. Dry down for LC-MS/MS. A dissolved peptide sample is then analyzed by a NanoLC-ESI-MS/MS system. NanoLC-ESI-MS/MS analysis of peptide samples is carried out by a high pressure liquid chromatography (HPLC) system (Agilent) with a 75 micrometer inner diameter 8cm in length reverse phase C18 column. The particle size of the C18 is 3uM with pore size of 300 Ä. The injection time is 20 minute. The HPLC Solvent A is 97.5% water, 2% acetonitrile, 0.5% formic acid. HPLC Solvent B is 9.5% water, 90% acetonitrile, 0.5% formic acid. The gradation time was 60 minutes from 2% Solvent B to 90% solvent B, plus 20 minutes for sample loading and 20 minutes for column washing. The column flow rate is around 800 nanoliter per minute after splitting. Typical injection volume is 3 ul. The HPLC system is on-line coupled with an ion trap mass spectrometer (QE, Thermo) in a way a sample eluted from HPLC column is directly ionized by an electrospray ionization (ESI) process and enter into the mass spectrometer. The ionization voltage is often optimized each time and normally in a range of 1.2kv-1.8kv. The capillary temperature is set at 110C. The mass spectrometer is set at the data-dependent mode to acquire MS/MS data via a low energy collision induced dissociation (CID) process. The default collision energy is 33% and the default charge state is 3.One full scan with 1 microscan with a mass range of 350 amu to 1100 amu is acquired, followed by one MS/MS scan of the most intense ion with a full mass range and three microscans. The dynamic exclusion feature is set as following: repeat count of 1 within 0.3 min and exclusion duration of 0.4min. The exclusion width is 4Da.PrideNot availableAs default, the mass spectrometric data is used to search against the most recent non-redundant protein database (NR database, NCBI) with ProtTech’s ProtMody software suite. The output from the database search was manually validated by a Sr. scientist before reporting. The parameters of the data acquisition and data processing are as following: Data acquisition parameters: Instrument: LTQ Software: Xcalibur 2.0 Centroid mode Minimum MS signal for Precursor-ion: 5x104 counts Processing parameters: Software: ProtMody 2.0 Signal-to-noise: >=5 De-isotoped: Yes Filtered: Yes Modifications: Cys 0 Database: protein database from UniProt DatabaseProteomicsJar-How LeeTerasaki Innovation Center, United StatesPARTIALHomo Sapiens (human)Not availablejarhowlee@tictx.orgTerasaki Innovation CenterUnited StatesWater, sodium salt, l(4)17, l(4)13, ammonium formate, Gli, Size, 13C-labeled, MeCN, cadmium salt, ion, TFA, Cid[Mel], Ci[D], Particle, H(2)O, BOUND WATER, magnesium formate, Capillary, oxidane, zinc salt, Solvent, CENP-A, Long Term, RP11-508D10.1, WATER, CENP-C, HOH, 5730420M11Rik, Polypeptides, M(3L)i, cobalt(II) formate dihydrate, CH3-C#N, Beds, B1, High Performance Liquid Chromatography, WMS, SET, type 5 acid phosphatase, pore, BcDNA:RE21270, C79325, rya-r44F, DmelCG13176, M, ORF19, Sinusoidal Bed, D17Mit170, HPLC, Rya-R44F, Bed, DmelCG4299, AI047805, set, T-cell antigen Gp39, CI, CG10844, column, ACN, D1, Acn, sample, Chromatography, High Speed Liquid, D9, TNFSF5, M(3)RpS17, nickel salt, SGS, CiD, LC-MS2, Ce, Ci, anatomical protrusion, cobalt (+2) salt, Tnfrsf5, Liquid Chromatography, Longterm Effect, Sinusoids, Tl3, Tl2, not genetically inherited, collisionally activated dissociation, Cid, CID, ciD, hCD40L, ACMICD, H2O, sodium (4:1:1) salt, count, magnesium salt, Dm1, M(3)i(55), Sizes, IMD3, ci-D, 1110049F14Rik, Hydrogen Oxide, rpS17, HLA-DR-associated protein II, DI-2, CENP-A/Cid, CENP-A/CID, CENPA, I-2Dm, formate, NKTL, cromium (+3), I-2PP1, TAF-IBETA, liquid chromatography-tandem mass spectroscopy, Charges and Fees, ammonium (4:1) salt, TAF-Ibeta, methyl cyanide, lead (+2) salt, Ci-155, Particle Sizes, nickel formate dihydrate, lead formate, Effects, Ly62, TAPK, aluminum salt, TR-AP, 17alpha)-isomer, CG7826, agua, CenpA, M(3)i, LC-MSMS, GP39, CG7835, Capillary Bed, CG42273, Siah, gp39, micrometre, CD154, anatomical systems, FAM39E, CATC4, GKLP, Acinus, Longterm, thallium (+1) salt, Sinusoidal Beds, rubidium salt, 2pp2a, Long-Term, l(3)dtOA4, methanoic acid, ions, High-Performance Liquid Chromatographies, CG10574, acinusL, Injectable, PCTAIRE2-binding protein, MGC:45012, 2PP2A, acinusS, M(3)i[55], dSET, dSet, CG2125, DmelCG10844, peptidos, UPLC, PTHB1, NTKL, DRR, cou, 1-(14)C-labeled, DRY, potassium formate, copper (+2) salt, ACP5, acetonitrile, SPENCDI, mKIAA0670, CD142, polypeptide, Wash2, Wash1, Lr, Temperatures, dry, I-2PP2A, ci[D], C18, ME-IV., cupric formate, chemical analysis, Long Term Effects, Dm I-2, 5alpha, BcDNA:RE44119, MFS1, aluminum formate, Sinusoidal, nl, AU020952, l(2)k00424, lithium formate, DmelCG2125, CenH3, ci155, IS-33, ensemble, M(3)q, pore-forming toxin activity, ethanenitrile, micron, anon-EST:Posey48, Longterm Effects, l(2)k04913, High Pressure, Capillary Beds, Fees, M(3L)i[55], Bra, liquid chromatography tandem mass spectrometry, TRACP, [OH2], CenpA/CID, channel-forming toxin activity, liquid chromatography tandem mass spectroscopy, Rps17, IPP2A2, NCMe, determination, RPS17, zinc formate, lead salt, peptide, M(3)67, Tnfsf5, ammonium tetraformate, peptido, BANF, Min, Injectables, Effect, DmelCG42273, T-BAM, CG13329, 3-hydroxy-5-estrane-17-carbonitrile, me75, LCMSMS, tartrate-resistant acid ATPase, peptides, TAF-I, 2610036I19Rik, l(3)67BDo, 2610510L13Rik, min, mAPC, µm, copper, SCAN, T1, TRAP3, IGAAD, fSAP152, lithium salt, Tudor repeat associator with PCTAIRE-2, High-Performance, DmelCG10574, dya, Cenp-A, dihydridooxygen, TF, High-Performance Liquid, blood capillary, dihydrogen oxide, T5ap, MGC - 45012, GPHYSD2, Long-Term Effects, ammonium (2:1) salt, Sinusoid, CD40L, phapii, LC-MS/MS, aqua, Cd40l, M(3)67C, Dmel_CG7826, StF-IT-1, um, Ionen, TNF-related activation protein, WASH, nickel (+2) salt, Ly-62, Dmel_CG7835, cenpA, Mnb, MNB, ammonium salt, CenH3/CID, Ci/Gli, Ci/GLI, RyR, MS/MS, Rp S17, hydrogen hydroxide, cobaltous formate, AW743063, tilorone analog IS-33, CG4299, MASS, AI326936, AW124434, acqua, Charge, RYR, Ryr, spine, TrATPase, copper salt, IGM, Liquid, CD40LG, Polypeptide, Wasser, i2pp2a, ryr, TRAP, p50, cesium salt, FBN, ACINUS, PHAPII, LC-MS-MS, formic acid, protrusion, l(4)102ABc, M(3)S33, potassium salt, Injection, ECTOL1, p63, 14C-labeled, p65, RyRs, Low, CD40-L, CenH3[Cid], CenH3[CID], MS2, iones, ipp2a2, DmelCG13329, Minute, eau, calcium formate, Charges, OCTD, X-linked combined immunodeficiency, Fee, DmelCG3922, TEIF, Trap, taf-ibeta, Ultra Performance Liquid Chromatography, HIGM1, Long-Term Effect, cromium (+3) salt, sodium formate, C78062, High-Performance Liquid Chromatography, P105, DYRK1, nickel formate, 3H-labeled, PCTAIRE2BP, igaad, strontium formate, cenH3, Bp50, strontium salt, Peptide, group, LC/MS/MS, capillary vessel, CAD, Ci155, water, I2PP2A, Dyrk1, (3alpha, ACETONITRILE, tandem MS, cyanomethane, WMS2, CG13176, dRyR, CC1, sample population, chromic formate, CG3922, dSET/TAF-Ibeta, 2610030F17Rik, Pressures, Ion, SSKS, calcium salt, Peptid, High Performance Liquid, assay, SCH, AA407739, 3-OHECN, Rya-r76CD, CID/CENP-AZip, ZIP, sMHC, Ifm(2)RU1, Dm II, MHC, determination, Stp, DroMII, Proteins, Mhc-c[1], Gene, Myo-II HC, E(br), Bsh, ifm(2)RU1, myoII, Sht, QA1, Myo, Dm nmII, nmMHC, mhc, ifm(2)2, chemical analysis, Protein, Gene Products, Mhc-c, EA2.1, CG15792, FBgn0002741, DmelCG15792, CG17927, mMHC, MRP, Mrp, Myo-II, Myo2, Ifm(2)2, Protein., l(2)M66, zip/MyoII, DmMHC, DROMHC, DmelCG17927, Protein Gene Products, NMMII, Gene Proteins, MyHC, ifm(2)RU2, Nup, NMM, HLA-6.2, Dronm-MII, anon-WO0140519.37, EA1.2, DmnmII, assay, MyoII, l(2)k10423, Mhc36B, Myo II, zpr, nmy-2, l(2)02957, l(2)36AeE 920, ion, instrument configuration, L-Zystein, FBN, Gene, p60c-yes, protein, Computer, precursor, protein-containing complex, hardware, ECTOL1, Gene Products, F15E12.6, Software Engineering, 2-amino-3-mercaptopropanoic acid, Cystein, protein aggregate, WMS, Computer Program, Application, Open Source Softwares, C, F15E12_6, MUB3_18, cisteina, Software Application, iones, E-920, Open, Open Source Software, Computer Programs and Programming, HardwareType, Hcys, MUB3.18, ions, Computer Software Application, OCTD, data processing, Tools, CYSTEINE, FREE CYSTEINE, (2R)-2-amino-3-mercaptopropanoic acid, GPHYSD2, SGS, Applications Software, p61-Yes, Open Source, Noise, Computer Software, protein complex, PRO, Proteins, Pollution, Data Base., CYS, Cys, Source Softwares, Software Tools, Tool, ACMICD, Programs, Program, Computer Applications, Software Tool, native protein, Ionen, Protein, Computer Applications Software, Computer Applications Softwares, MFS1, Softwares, (2R)-2-amino-3-sulfanylpropanoic acid, Software, and GLY protein 2, Zystein, WMS2, Data Base, ATCMPG1, MET, ATCMPG2, parent ion, and GLY protein 1, Software Applications, YES, Yes, instrument, 2-amino-3-sulfanylpropanoic acid, Source Software, HsT441, Engineering, L-2-Amino-3-mercaptopropionic acid, c-Yes, (R)-2-amino-3-mercaptopropanoic acid, MASS, 2-Amino-3-mercaptopropionic acid, Noises, L-Cystein, Protein Gene Products, Computer Programs, Gene Proteins, data analysis, Applications, P61-YES, yes, Applications Softwares, precursor ion, Ion, SSKS, E920, c-yes, Noise Pollution, Computer Software ApplicationsInfectious Mononucleosis Viruses, B Cells, B Lymphocytes, protein complex, Burkitt's Lymphoma Virus, Proteins, B cell, Infectious, Gene, protein, protein-containing complex, Peptide, E-B Virus, Bursa-Dependent Lymphocytes., Herpesvirus, Human, Polypeptides, Epstein-Barr Virus, peptido, native protein, Protein, Epstein Barr Virus, Gene Products, Burkitt Lymphoma Virus, protein aggregate, Mononucleosis Viruses, E-B Viruses, Mononucleosis Virus, Burkitts Lymphoma Virus, B-cell, Burkitt, peptides, Bursa-Equivalent Lymphocyte, EBV, E B Virus, Human Herpesvirus 4, Protein Gene Products, Gene Proteins, Burkitt Herpesvirus, HHV-4, B lymphocyte, B-Lymphocyte, Infectious Mononucleosis Virus, Herpesvirus 4 (gamma), Peptid, peptidos, Polypeptide, Lymphoma Virus, B-lymphocytefalseMHC peptidome analysis of HLA DQβ0603:DQα0103 proteinsIdentification of Peptides associated with HLA-Class 2 protein, DQβ0603:DQα0103, from two different EBV transfromed B cell lines, 9060 and 9062.2023-11-252023-07-22PXD043999NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:43186NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:1367269NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1436733NEWT:460519NEWT:1247411NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:84588NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:215402NCBITaxon:548681NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:1034015NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:74649NEWT:52638NEWT:57075NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:5322NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:553470NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:231490NEWT:244704NEWT:7725NEWT:430615NEWT:563041NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEW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