Reproducibility Crossroads: Impact of Statistical Choices on Proteomics Functional Enrichment.

ABSTRACT: Quantitative proteomics relies on robust statistical methods for differential expression, critically impacting downstream functional enrichment. This meta-analysis systematically investigated how statistical hypothesis testing approaches and criteria for defining biological relevance influence functional enrichment concordance. We reanalyzed five independent label-free quantitative proteomics datasets using diverse frequentist (t-test, Limma, DEqMS, MSstats) and Bayesian (rstanarm) approaches. Concordance of Gene Ontology (GO) and KEGG pathways was assessed using Jaccard indices and correlation metrics, grouping comparisons by statistical test and biological relevance consistency. The results demonstrated highly significant differences in similarity distributions among the compariso

SUBMITTER: Biello KA 

PROVIDER: S-EPMC12471179 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature