{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T22:50:03Z","timestamp":1792104603852,"version":"4.4.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":265,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UU_00025\/7"],"award-info":[{"award-number":["MC_UU_00025\/7"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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\u2013based 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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 adenocarcinoma cells.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbag278","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T12:02:02Z","timestamp":1790164922000},"source":"Crossref","is-referenced-by-count":0,"title":["OOPSIE (OOPS informatics extension)"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1288-9172","authenticated-orcid":false,"given":"Stephanie B","family":"Telerman","sequence":"first","affiliation":[{"name":"Department of 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