OOPSIE (OOPS Informatics Extension)

Clicks: 21
ID: 329511
2026
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Abstract
Abstract Motivation The RNA-bound proteome represents a dynamic and pleiotropic network of RNA-binding proteins (RBPs) that integrate diverse cellular pathways. RNA-binding dynamics profiling using cross-linking–based enrichment strategies including Orthogonal Organic Phase Separation (OOPS), generates complex peptide-level quantitative mass spectrometry datasets, yet dedicated computational workflows for standardized normalization and differential analysis remain limited. Results OOPS relies on phase partitioning of RNA binding proteomes, upon UV cross-linking. As glycoproteins have been shown to co-partition independently of cross-linking due to their physicochemical properties, they provide a cross-link-independent reference population that can be leveraged for normalization of RNA-binding-dependent changes. We introduce OOPSIE (Orthogonal Organic Phase Separation Informatics Extension), an R-based script that provides a reproducible framework of peptide-level OOPS-derived data using protein-level normalization and differential analysis of RNA-binding capacity. We demonstrate its utility using OOPS-derived datasets generated from A549 lung carcinoma cells. Availability and implementation OOPSIE is implemented in R as a standalone workflow and is freely available at https://github.com/CambridgeCentreForProteomics/oopsie, together with documentation and example datasets.
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Authors Stéphanie B. Telerman, Lajos Kalmár, Sandip K Patel, Anne E. Willis, Kathryn S Lilley
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Journal Bioinformatics advances
Year 2026
DOI
10.1093/bioadv/vbag278
URL
https://doi.org/10.1093/bioadv/vbag278
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