This is a table of the raw apLCMS-based peak intensity extraction of HRMS results, including blank (Water) and quality control (NIST, QSTD) samples. Total features detected, 11,188. “NIST” refers to the SRM 1950 reference standard. “QSTD” refers to an in-house prepared mixture of human plasma. All samples were injected in triplicate and the results have been median summarized from the triplicates. The first two columns pertain to the detected m/z value at a specific retention time, given in seconds. The remaining columns pertain to blanks, reference standards and samples. These columns are ordered left-to-right in the order of injection. For the samples, “_A” or “_B” designations pertain to shipment batches that took place between Erasmus and Emory. Three samples were ultimately excluded from analysis: one, 25, because of aberrant global sample composition, and two others, 09_A and 15_A, because aliquots were accidentally shipped and processed two independent times because the samples were blinded. For subsequent analyses, we arbitrarily kept 09_B and 15_B samples from the second batch and discarded their “_A” counterparts, as the “_B” versions were believed to have undergone fewer freeze-thaw cycles than “_A” samples. [This file description may also be found in the Supplementary Information of the corresponding publication.]

This is the results file of the untargeted analysis using an in-house R package (https://github.com/kuppal2/xmsPANDA) on raw HRMS data after removing features that did not meet data quality thresholds and dropping poor quality and redundant samples. QC materials were not analyzed in the untargeted test. Columns A-B pertain to observed m/z and retention time. Columns C-E pertain to accurate mass matches to the features (Annotation, Adduct, and ppm mass accuracy error; see Supplementary Methods for details). After accurate mass matching, spectral convolutions (i.e., isotopes and neutral losses) were designated by manual inspection of co-elution, intensity correlation and m/z shift. Retention times were taken into consideration for assignments (e.g., longer retention times generally correspond to hydrophilicity and spectral convolutions of adducts and isotopes should co-elute). Note, the [M+H] ion of lidocaine (235.1804 m/z by 127.6 sec; used as local anesthetic during bronchoscopy) held the maximum intensity value in each sample and was normalized to the same maximal value in each distribution, resulting in its removal during testing. Ppm error was calculated by METLIN except for spectral convolutions, which were calculated manually. Accurate mass annotations are only provided for those results that met significance criteria (p < 0.05, q < 0.25). Columns F-H indicate the raw p-value (“P.value”), q-value (“adjusted.p.value”) and Pearson’s r statistic (“Estimate_var1”), respectively. Remaining columns show log2-transformed and quantile normalized HRMS intensities for each of the study samples. Missing values were imputed as “NA” to avoid skewing the correlation. The sample columns were automatically ordered from low-to-high PRAGMA-%Dis. [This file description may also be found in the Supplementary Information of the corresponding publication.]

These data correspond to important clinical variables for the patient samples analyzed in this study. [This file description may also be found in the Supplementary Information of the corresponding publication.]

Results used for follow-up studies with Spearman’s correlations. MetO and methionine (Met) quantifications are based on reference calibration relative to the concentrations determined for SRM 1950 reference material. MPO measurements are based on the ELISA assay. [This file description may also be found in the Supplementary Information of the corresponding publication.]