PNNL

Abstract

Methods for detecting differentially abundant proteins between samples in label-free LC-MS pro-teomics experiments rely on statistically testing inferred protein abundances derived from peptide ionization intensities. Here, we statistically test peptide ionization intensities directly and com-bine the resulting dependent P-values using the Empirical Brown’s Method (EBM), avoiding error introduced through the estimation of protein abundances. We show that a peptide-level approach using EBM outperforms a standard proteomics differential abundance analysis using protein-level LFQ intensities. Additionally, we show the effectiveness of this approach in detecting enriched proteins from a targeted activity-based protein profiling dataset.