ArticlePLoS computational biology2022
Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A Bayesian framework for multivariate differential analysis.PLoS computational biology · 2026Article
- cpiVAE: Robust and Interpretable Cross-Platform Proteomics Imputation.bioRxiv : the preprint server for biology · 2025Article
- AUGMENTED DOUBLY ROBUST POST-IMPUTATION INFERENCE FOR PROTEOMIC DATA.The annals of applied statistics · 2025Article
- AUGMENTED DOUBLY ROBUST POST-IMPUTATION INFERENCE FOR PROTEOMIC DATA.bioRxiv : the preprint server for biology · 2025Article
- Optimizing imputation strategies for mass spectrometry-based proteomics considering intensity and missing value rates.Computational and structural biotechnology journal · 2025Article
- Challenges and Opportunities for Single-cell Computational Proteomics.Molecular & cellular proteomics : MCP · 2023Review
- Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly.International journal of molecular sciences · 2023Article
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Authors and funding
3 authors.
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Abstract
Imputing missing values is common practice in label-free quantitative proteomics. Imputation aims at replacing a missing value with a user-defined one. However, the imputation itself may not be optimally considered downstream of the imputation process, as imputed datasets are often considered as if they had always been complete. Hence, the uncertainty due to the imputation is not adequately taken into account. We provide a rigorous multiple imputation strategy, leading to a less biased estimation of the parameters' variability thanks to Rubin's rules. The imputation-based peptide's intensities' variance estimator is then moderated using Bayesian hierarchical models. This estimator is finally included in moderated t-test statistics to provide differential analyses results. This workflow can be used both at peptide and protein-level in quantification datasets. Indeed, an aggregation step is included for protein-level results based on peptide-level quantification data. Our methodology, named mi4p, was compared to the state-of-the-art limma workflow implemented in the DAPAR R package, both on simulated and real datasets. We observed a trade-off between sensitivity and specificity, while the overall performance of mi4p outperforms DAPAR in terms of F-Score.
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