Supplementary metabolomics datasets for Paired cerebrospinal fluid metabolomic changes across repeated anodal transcranial direct current stimulation in Parkinson's disease: an exploratory within-subject study

This dataset supports the revised manuscript entitled “Paired cerebrospinal fluid metabolomic changes across repeated anodal transcranial direct current stimulation in Parkinson’s disease: an exploratory within-subject study.” The dataset contains feature-level and participant-level cerebrospinal fluid (CSF) metabolomics data acquired before and after five consecutive daily sessions of anodal transcranial direct current stimulation (tDCS) in patients with Parkinson’s disease. Polar and non-polar fractions were analyzed separately using ion mobility-enabled UPLC-QTOF mass spectrometry. This new version has been updated to reflect the final paired within-subject analytical workflow used in the revised manuscript. For the polar dataset, 201 annotated features are provided, of which 156 passed analytical-quality criteria; 16 features met the predefined robust-candidate criteria. The primary analysis was based on 12 complete Pre/Post pairs, with two additional Pre-only profiles retained for an all-profile generalized estimating equation sensitivity analysis. For the non-polar dataset, the revised analysis includes 189 annotated features and explicitly incorporates the available technical-injection structure. Injection-level sample-median scaling was applied before technical-replicate averaging for the primary analysis. Of 189 annotated non-polar features, 169 passed analytical-quality criteria, 17 were supported after Benjamini-Hochberg false discovery rate correction, and 14 met the predefined primary-candidate criteria. Twelve of these 14 candidates also met the alternative probabilistic quotient normalization (PQN) candidate criteria, while one candidate also met the unnormalized duplicate-averaged raw-log criteria. The uploaded workbook includes sample metadata, raw injection-level intensity matrices, participant-level processed matrices, normalization factors, complete annotation and analytical-quality information, all-feature statistical results, concise summaries of statistically supported polar and non-polar features, dataset notes, and a data dictionary. Unmatched post-intervention values were not imputed, and technical injections were not treated as independent biological observations. This dataset is intended to provide transparent supporting data for the exploratory within-subject analyses reported in the revised manuscript. Because the study did not include a sham-control group, the observed metabolomic differences should not be interpreted as evidence of treatment efficacy or tDCS-specific causality.