{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD051982/report.pg_matrix.tsv"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD051982/metadata_chicago.txt"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD051982/DAC_Chicago_cohort.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["herbert.schiller@helmholtz-munich.de"],"submitter":["Anna Semenova"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"disease":["Bacterial Pneumonia","Covid-19","Influenza"],"software":[""],"submitter_keywords":["Covid-19","Dac"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD051982"],"tissue":["Blood Plasma","Blood Serum"],"sample_protocol":["The assay is based on immunoprecipitation and utilizes Protein L agarose-coupled beads (Pierce, Thermo Fisher Scientific, Germany) to capture antibodies of IgG, IgA, IgM, and IgD isotypes from serum. After purification, antibodies on the beads are incubated with a protein extract of ‘healthy’ lung tissue to initiate capture self-antigens followed by mass spectrometric identification of the assembled protein complexes. Digested peptides were separated by nanoflow reversed-phase chromatography for the DAC samples using an Evosep One liquid chromatography (LC) system (Evosep). The separation occurred on an 8 cm × 150 um column packed with 1.9 um ReproSil‐Pur C18‐AQ particles (Dr. Maisch) applying the 60 SPD method with a 44-minute gradient. The mass spectrometer was operated in diaPASEF mode with a full scan range of 100–1,700 m/z with a ramp time of 100ms, ion mobility was set between 0.7 to 1.45 1/K0. 27 diaPASEF windows followed one full scan in 9 acquisition frames. The DIA window ranged from 300 m/z to 1110 m/z with an isolation window of 30 Da. The collision energy was set dynamically."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The DAC raw mass spectrometry files were processed with DIA-NN (v.1.8.1)71. During processing, filtering was applied at multiple levels, including precursor level q-value (1%), library q-value (0.5%), and gene group q-value (1%). Enzymatic cleavage was defined by Trypsin/P and LysC proteases with match-between-runs (MBR) mode enabled for the library-free searches. Methionine oxidation and N‐terminal acetylation were selected as variable modifications. All other processing parameters were kept by standard settings of the DIA-NN version utilized in the analysis."],"omics_type":["Proteomics"],"labhead":["Dr. Herbert Schiller"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Director, Research Unit for Precision Regenerative Medicine, Helmholtz Munich Professor, Systems Biology of Airways and Lungs, Ludwig-Maximilians University (LMU) Munich Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL) (lab head)"],"species":["Homo Sapiens (human)"],"submitter_mail":["anna.semenova@helmholtz-munich.de"],"publication":["Not available"],"submitter_affiliation":["Helmholtz Munich, Institute of Lung Health and Immunity"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Differential antibody capture pneumonia samples Chicago cohort","description":"We performed a DAC assay for both cohorts to obtain autoantibody binding profiles. The assay is based on the immunoprecipitation of immunoglobulins from the serum/plasma of the patients and subsequent incubation with a pool of tissue proteins. In the case of the COVID-19 experiment, we selected the lung as a target tissue due to the high involvement in the pathology of this infection. The lung tissue pool was obtained by homogenizing peritumoral lung tissue from 32 donors.","dates":{"publication":"2026-04-14","submission":"2024-05-04"},"accession":"PXD051982","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:1247","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:9644","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:27592","NEWT:98334","NEWT:426428","NEWT:588858","NEWT:9639","NEWT:242231","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:2172103","NEWT:7460","NEWT:6491","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NEWT:13164","NEWT:216129","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:1194669","NEWT:243230","NEWT:8355","NEWT:633","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:8479","NEWT:1283300","NEWT:632","NEWT:6183","NEWT:6063","NEWT:630","NEWT:334747","NEWT:61235","NEWT:15368","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:469008","NEWT:260707","NEWT:256318","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:1719","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:105231","NEWT:52638","NEWT:4097","NCBITaxon:6073","NEWT:884204","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NEWT:607699","NCBITaxon:1502","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:38783","NEWT:8727","NEWT:4006","NEWT:8726","NEWT:6426","NEWT:6669","NEWT:10090","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:5334","NEWT:37334","NEWT:382352","NCBITaxon:10359","NEWT:242619","NEWT:632957","NEWT:34073","NEWT:373995","NEWT:544404","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:2758385","NEWT:37349","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:714","NEWT:421932","NEWT:312017","NEWT:196627","NEWT:5691","NEWT:48479","NEWT:627025","NEWT:1097677","NEWT:61674","NEWT:1117957","NEWT:9913","NEWT:8709","NEWT:4100","NEWT:2666255","NEWT:1159556","NEWT:1076","NEWT:6763","NEWT:803","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:981087","NEWT:180066","NEWT:468911","NEWT:7604","NEWT:135588","NEWT:1843183","NEWT:58002","NEWT:326423","NEWT:36111","NEWT:4577","NEWT:1416333","NEWT:5664","NEWT:2157","NEWT:1678078","NEWT:749906","NEWT:418985","NEWT:146479","NEWT:749907","NEWT:1911079","NEWT:69373","NEWT:264203","NEWT:1480154","NEWT:1274414","NEWT:27606","NEWT:59202","NEWT:9975","NEWT:9612","NEWT:38865","NEWT:51953","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:112273","NEWT:36329","NEWT:1147787","NEWT:62615","NCBITaxon:3044782","NEWT:1440772","NEWT:72407","NEWT:1355477","NEWT:349741","NEWT:9605","NEWT:9606","NEWT:90371","NEWT:157295","NEWT:641501","NEWT:7668","NEWT:915099","NEWT:74940","NEWT:9721","NEWT:137221","NEWT:9600","NEWT:9963","NEWT:1450511","NEWT:1143193","NEWT:1617910","NEWT:565050","NEWT:411901","NEWT:9838","NEWT:105884","NCBITaxon:9615","NEWT:9839","NEWT:58334","NEWT:1193501","NEWT:3055","NEWT:58331","NEWT:6326","NEWT:6689","NEWT:5476","NEWT:1450520","NEWT:299767","NEWT:1274432","NEWT:1274426","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:393765","NEWT:698936","NEWT:39946","NEWT:9823","NEWT:9940","NEWT:95602","NEWT:8732","NEWT:521001","NEWT:39947","NEWT:224911","NEWT:1274420","NEWT:578458"],"ORCID":["0000-0001-8476-2341"]}}