A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics

In this study, we thoroughly characterized ion interference at the MS2 level using a defined two-proteome experimental system with known ground-truth. We discovered remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2-scans - a discrepancy that we found resolved by considering co-fragmentation of peptide ions hidden within the spectral "noise" of the MS1 isolation window. To address this issue, we developed a regression modeling strategy to accurately predict reporter ion interference in any dataset. Finally, we demonstrate the utility of our procedure for improved fold change estimation and unbiased PTM site-to-protein normalization. All computational tools and code required to apply this method to any MS2 TMT dataset are documented and freely available.PMID:38097181 | DOI:10.1016/j.mcpro.2023.100694
Source: Molecular and Cellular Proteomics : MCP - Category: Molecular Biology Authors: Source Type: research