{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/Serum_MAgNet_enrichment.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/Serum_EVs_SEC.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/Cell_line_EVs_SEC.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/Plain_serum_digestion.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/250306_OCI_LY7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/250306_U_2932.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/250306_SUDHL_4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/250306_Riva.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/SEC_EV_folders_zipped.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075504/MAgNet_and_plain_serum_files_zipped.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["saara.hamalisto@utu.fi"],"submitter":["Saara Hämälistö"],"technology_type":["Mass Spectrometry","Data-independent acquisition"],"software":[""],"submitter_keywords":["Human lymphoma extracellular vesicle"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075504"],"tissue":["Cell Culture","Blood Serum"],"sample_protocol":["Isolated EVs were lysed in a buffer containing 8 M urea, 0.5% NP40, 150 mM NaCl, and 1X protease inhibitors for 30 minutes on ice. The samples were sonicated for 5 minutes (30 s on and 30 s off), and the proteins were precipitated using 4-5 volumes of cold acetone overnight at -20 °C. The samples were cleared by centrifugation for 15 minutes at 16,000 × g and 4 °C, and the pellet was dissolved in 100 µL of 8 M urea in 50 mM ammonium bicarbonate. All of the samples were used for in-solution digestion. The samples were reduced with 10 mM DTT for 1 hour at 37 °C and alkylated with 40 mM IAA for 1 hour in the dark. The alkylation was quenched with 40 mM DTT, and the urea concentration was diluted by adding 900 µL of 50 mM ammonium bicarbonate. Sequencing-grade trypsin was added to each sample in a 1:30 ratio, and the samples were incubated overnight at 37 °C. After digestion, the peptide samples were acidified to 1% trifluoroacetic acid (TFA) concentration (pH 2), desalted using a Sep-Pak tC18 96-well plate (Waters), and evaporated to dryness.  For MagNet enrichment, equal volumes of the samples were mixed with binding buffer to a final volume of 50 µL. Then, 2 µL of MagReSyn SAX beads (ReSyn Biosciences) were added and mixed by pipetting. Reduction, alkylation, and wash steps were performed using an Opentrons pipetting robot (Opentrons, New York, United States) following the Proteomics Facility’s MagNet enrichment protocol. In the final step, sequencing-grade modified trypsin (Promega) was added, and the sample plate was incubated overnight at +37 °C. On the following day, half of each sample was loaded onto Evotip Pure tips (Evosep) and analyzed using a TimsTOF mass spectrometer.  The LC-ESI-MS/MS analysis was performed on Evosep One HPLC system (Evosep, Odense, Denmark) coupled to the timsTOF fleX mass spectrometer (Bruker, Bremen, Germany) equipped with a CaptiveSpray nano-electrospray ionization source. Peptides were separated inline on a 15 cm Evosep Performance column (150 μm x 15 cm, 1.5 μm C18-beads, EV1137). The mobile phase consisted of water with 0.1% formic acid (solvent A) and 0.1% formic acid/99.9% acetonitrile (v/v) (solvent B). Samples were analyzed with 44 min 30 samples per day method. Samples were analyzed by a data independent acquisition (DIA) LC-MS/MS method. MS data was acquired automatically by using Compass 2025 software (Bruker). The DIA method covered a m/z range from 350 to 1100 and included two ion mobility (IM) windows per dia-PASEF scan with variable isolation window widths adjusted to the precursor densities. Twenty-five dia-PASEF scans were deployed, and IM range was set to 1.3 and 0.6 Vcm-2. Accumulation and ramp times were specified as 100 ms."],"repository":["Pride"],"modification":[""],"quantification_method":["Not available"],"data_protocol":["Data analysis consisted of protein identifications and label free quantifications of protein abundances. Data was analyzed by Spectronaut software (Biognosys)."],"omics_type":["Proteomics"],"labhead":["Saara Hämälistö"],"instrument_platform":[""],"labhead_affiliation":["University of Turku, Institute of Biomedicine, Finland"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["saara.hamalisto@utu.fi"],"publication":["Not available"],"submitter_affiliation":["University of Turku and FICAN West"],"submitter_country":["Finland"],"additional_accession":[]},"is_claimable":false,"name":"Analysis of lymphoma EV and serum samples","description":"Detecting extracellular vesicle-related markers in EV samples extracted from human lymphoma cell lines and EVs enriched from serum samples.","dates":{"publication":"2026-03-26","submission":"2026-03-11"},"accession":"PXD075504","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:4081","NEWT:876138","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","NEWT:61235","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:44685","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:2758385","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:8022","NEWT:145943","NEWT:3635","NEWT:5811","NEWT:1480154","NEWT:235443","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"],"ORCID":["0000-0001-5348-4422"]}}