提出多宇宙共识流程,让代谢组学特征选择结果更可复现。
A multiverse-consensus pipeline for reproducible feature selection in untargeted LC-MS metabolomics

- 构建十阶段质控流水线,全程记录每个特征的去留
- 在四种预处理策略下运行多路径分析,仅保留跨路径共现特征
- 适合关注结果稳健性的代谢组学研究者,尤其看重可复现性
未靶向液相色谱-质谱代谢组学需要一系列预处理决策,每一步都有多个合理选项。研究者通常选定一条流程并报告最终特征列表,但其对未被检验的选择敏感性难以察觉。本文将多宇宙分析引入未靶向代谢组学特征选择,提出一个可审计、配置驱动的流程:(i) 应用十阶段质量控制过滤器级联,记录每个特征的命运;(ii) 在四个不同预处理理念下,结合四种特征排序方法,通过自助稳定性选择和标签置换测试运行多路径下游分析。仅在多个路径中反复出现的特征进入分层共识。在5个乳腺癌细胞系数据集(30,370个检测特征)上,四条单一流程分别产出4–20个特征,两两间雅可比相似度低至0.05。多宇宙共识保留15个特征(≥2/4路径),其中1个贯穿所有路径,但两条共享归一化与漂移校正方法的路径主导共识。全管道标签置换测试在50次零假设置换中未发现假阳性。结论:报告仅基于预处理稳健的特征,并提供完整保留/剔除审计日志,可将隐藏的分析自由度转化为显式可审查输出。讨论了局限性,包括单批次设计及需独立验证。
原文摘要 · Abstract (English)
Background: Untargeted LC-MS metabolomics requires a long chain of preprocessing decisions, each with several equally defensible options. Analysts typically commit to one pipeline and report the resulting feature shortlist. How strongly that shortlist depends on choices that were never varied stays invisible. Results: We adapt multiverse analysis to untargeted metabolomics feature selection. We present an auditable, configuration-driven pipeline that (i) applies a ten-stage quality-control filter cascade in which every feature's fate is logged, and (ii) runs the downstream analysis as a multiverse over four contrasting preprocessing philosophies, each combined with four feature-ranking methods under bootstrap stability selection and label-permutation testing. Only features recurring across paths enter a tiered consensus. On a demonstration dataset of five breast-cancer cell lines (30,370 detected features), the four single pipelines individually returned shortlists of 4-20 features whose pairwise agreement was as low as Jaccard = 0.05. The multiverse consensus retained 15 features (>=2/4 paths), of which one recurred across all four, although two paths (sharing normalization and drift-correction methods) dominate the consensus. A pipeline-wide label-permutation test found no false discoveries in 50 null permutations. Conclusions: Reporting only preprocessing-robust features, with a complete kept/dropped audit trail, converts hidden analytical degrees of freedom into an explicit, inspectable output. We discuss scope and limitations, including single-batch design and the need for independent validation.
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