Psoriatic arthritis (PsA) clinical lipidomics dataset with hidden laboratory workflow artifacts

This dataset provides plasma lipidomic profiles from a cross-sectional cohort of patients with psoriatic arthritis (PsA) and healthy controls matched by age, sex, and BMI. Plasma samples were collected at University Hospital Frankfurt and the German Red Cross Blood Transfusion Service in Frankfurt, Germany, and analyzed on high-resolution mass spectrometry platforms (Thermo Fisher Q Exactive and Sciex QTRAP 6500+) using both targeted and untargeted lipid assays.

The dataset is organized into four comma-separated values (CSV) files containing Box-Cox-transformed and imputed lipidomics values, corresponding back-transformed measurements on the original scale, detailed clinical and analytical metadata including PsA status, ESOM-based classes, sex, and assay-specific batch identifiers, and variable-level descriptions for all 292 lipids.

Across all files, 292 plasma lipid species are included, named according to LIPID MAPS classification and standardized lipid nomenclature. The variables span major lipid classes such as carnitines, ceramides, glycerophospholipids, sphingolipids, glycerolipids, fatty acids, sterols and esters, and endocannabinoids.

Because the dataset contains an embedded batch structure, it is not intended for deriving new biological conclusions. Instead, it serves as a resource for methodological research on data quality control, batch effect identification, evaluation of preprocessing pipelines, and assessment of how sampling and processing parameters influence analytical robustness.

The dataset consists of four CSV files:

"PsA_lipids_BC.csv"
Contains the primary lipidomics data matrix with 107 subjects and Box-Cox-transformed, outlier-cleaned, and imputed plasma lipid measurements for 292 lipids.

"PsA_lipids_orig_values.csv"
Contains the same subjects and variables as above, but values are back-transformed to the original measurement scale following outlier removal and imputation, preserving identical identifiers and structure.

"PsA_classes.csv"
Provides 107 rows and 12 columns of metadata linking each subject to clinical (PsA vs. control), ESOM-based, and gender classifications, as well as six assay-specific batch identifiers. Columns 11 and 12 include the sampling date and weekday for control samples, enabling investigation of temporal or workflow-related effects.

"readme.csv"
Contains 292 rows (matching the number of lipid variables) and 7 columns describing each lipid at the individual variable level: "variable_name" (lipid identifier), "unit" ("arbitrary" for screening = peak area relative to class-specific internal standard; "ng/mL" or "pg/mL" for targeted), "class_name" (e.g., "Fatty acids", "Lysophosphatidylcholine"), "class_code" (e.g., "FA", "LPC"), "analytical_method_category" ("Lipid screening" or "Lipid targeted"), "LLOQ", and "ULOQ" (quantification limits; NA for screening lipids).

本数据集提供了银屑病关节炎（psoriatic arthritis, PsA）患者横断面队列与按年龄、性别、体质量指数（body mass index, BMI）匹配的健康对照人群的血浆脂质组学图谱。血浆样本采集自德国法兰克福的法兰克福大学医院与德国红十字会输血服务中心，并采用靶向与非靶向脂质检测方法，在高分辨率质谱平台（赛默飞世尔Q Exactive、Sciex QTRAP 6500+）上完成分析。

本数据集包含4个逗号分隔值（comma-separated values, CSV）格式文件，分别存储经Box-Cox变换与缺失值插补的脂质组学数值、对应原始尺度的反变换测量值、详细的临床与分析元数据（涵盖PsA状态、ESOM分类、性别与检测特异性批次标识符），以及全部292种脂质的变量级描述信息。

本数据集全部文件共涵盖292种血浆脂质组分，其命名遵循LIPID MAPS分类体系与标准化脂质命名规则。所涉脂质类别涵盖肉碱类、神经酰胺类、甘油磷脂类、鞘脂类、甘油脂类、脂肪酸类、甾醇及其酯类，以及内源性大麻素类。

由于本数据集内嵌批次结构，因此不应用于推导全新的生物学结论，而是作为方法学研究的资源，可用于数据质量控制、批次效应识别、预处理流程评估，以及分析采样与处理参数如何影响分析稳健性的相关研究。

本数据集包含4个CSV格式文件：
"PsA_lipids_BC.csv"
包含核心脂质组学数据矩阵，涵盖107名受试者的292种血浆脂质检测值，这些数值已完成Box-Cox变换、异常值清理与缺失值插补。

"PsA_lipids_orig_values.csv"
与上述文件包含相同的受试者与变量，但数值已完成异常值移除与缺失值插补后，反变换至原始测量尺度，且保留完全一致的标识符与数据结构。

"PsA_classes.csv"
包含107行、12列的元数据，将每名受试者与临床分类（PsA患者 vs 健康对照）、ESOM分类、性别分类，以及6个检测特异性批次标识符相关联。其中第11、12列记录了对照样本的采样日期与采样星期，可用于探究时间或实验流程相关的效应。

"readme.csv"
包含292行（与脂质变量数量一致）、7列的内容，用于逐条描述每种脂质的变量级信息：包括"variable_name"（脂质标识符）、"unit"（检测单位：筛选类检测为“任意单位”，即相对于类别特异性内标的峰面积；靶向类检测为ng/mL或pg/mL）、"class_name"（例如“脂肪酸类”“溶血磷脂酰胆碱”）、"class_code"（例如"FA"、"LPC"）、"analytical_method_category"（“脂质筛选”或“靶向脂质检测”）、"LLOQ"（下限定量限（Lower Limit of Quantification, LLOQ））与"ULOQ"（上限定量限（Upper Limit of Quantification, ULOQ），筛选类脂质的该值为NA）。