A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics.

ABSTRACT:

Background

In bottom-up proteomics using data-independent acquisition mass spectrometry (DIA-MS), quantitative measurements are obtained following multiple steps of protein fragmentation and ionization, which introduces cumulative errors and impairs the effectiveness of classical statistical methods. This study proposes an alternative statistical approach for testing group mean differences at the peptide level in quantitative bottom-up proteomics.

Results

We present a novel probabilistic graphical model, that accounts for the non-normality of empirical distributions and the correlations between fragment ion quantities. Based on the model, we propose a new statistical method that improves upon the classical feature-based approach by incorporating distribution-free shrinkage e

SUBMITTER: Lee N 

PROVIDER: S-EPMC12577184 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature