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. 2022 Jul 21;18(10):1104–1114. doi: 10.1038/s41589-022-01062-y

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a, Schematic representation of the experimental design and data-analysis strategies. Fe-IMAC, Fe³⁺-immobilized metal ion affinity chromatography; p.pep, phosphopeptide; TMT, tandem mass tag; unmod., unmodified. b, Volcano plot of the differential solubility of phosphopeptides of a protein compared to its unmodified protein in RNA-preserved lysate. Phosphopeptides exhibiting significantly (|log₂ (FC)| > 0.5 and adjusted P value obtained from limma analysis (Benjamini–Hochberg) < 0.01) lower (orange) and higher (purple) solubility than the unmodified proteins are shown. c, Volcano plot of the differential RNA-bound fraction of phosphopeptides of a protein compared to its unmodified protein. Phosphopeptides exhibiting significantly (|log₂(FC)| > 0.5 and adjusted P value obtained from limma analysis (Benjamini–Hochberg) < 0.01) lower (red) and higher (blue) proportions in the RNA-bound subpool than the unmodified proteins are shown. d, Venn diagram summarizing the overlap in different categories of assigned phosphopeptides. e,f, Visualization of the median solubility profiles (n = 3) of identified phosphopeptides (solid lines, phosphosites as points) and unmodified protein (dashed line) in log₂ scale is represented along the linear sequence of the protein (x axis) of COIL (e), PRPF6 and PRPF31 (f). Top, schematic representation of the protein with its domains and known phosphosites from UniProt.

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