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Article Dans Une Revue Molecular and Cellular Proteomics Année : 2022

MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates

Arthur Declercq
Robbin Bouwmeester
Sven Degroeve
Lennart Martens
Ralf Gabriels

Résumé

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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Dates et versions

hal-03843119 , version 1 (08-11-2022)

Identifiants

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Arthur Declercq, Robbin Bouwmeester, Aurélie Hirschler, Christine Carapito, Sven Degroeve, et al.. MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates. Molecular and Cellular Proteomics, 2022, 21 (8), pp.100266. ⟨10.1016/j.mcpro.2022.100266⟩. ⟨hal-03843119⟩
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