Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD051982/report.pg_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD051982/metadata_chicago.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD051982/DAC_Chicago_cohort.zipprimaryOK200herbert.schiller@helmholtz-munich.deAnna SemenovaMass SpectrometryBottom-up proteomicsBacterial PneumoniaCovid-19InfluenzaCovid-19Dachttps://www.ebi.ac.uk/pride/archive/projects/PXD051982Blood PlasmaBlood SerumThe 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.PrideThe 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.ProteomicsDr. Herbert SchillerPARTIALDirector, 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)Homo Sapiens (human)anna.semenova@helmholtz-munich.deNot availableHelmholtz Munich, Institute of Lung Health and ImmunityGermanyfalseDifferential antibody capture pneumonia samples Chicago cohortWe 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 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