Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics

TL;DR

This paper introduces mi4p, a novel method for differential analysis in mass spectrometry-based proteomics that accounts for imputation uncertainty, improving accuracy over existing methods.

Contribution

The paper presents a rigorous multiple imputation strategy combined with Bayesian moderation, enhancing variability estimation and differential analysis in proteomics datasets.

Findings

mi4p outperforms DAPAR in F-Score on simulated and real data.

mi4p balances sensitivity and specificity effectively.

The methodology can be applied at peptide and protein levels.

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. For protein-level results based on peptide-level quantification data, an aggregation step is also included. 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.