Fig. 3: FLiP–MS captures known PBI changes in P-body protein complexes on DNA replication stress.

a, Volcano plot showing differential abundance analysis of peptides from LiP–MS on HU-induced DNA replication stress. Peptide abundances were corrected for protein abundance changes between conditions. P values were calculated by an ANOVA (one-way) and corrected for multiple testing (Benjamini–Hochberg). The dotted horizontal line indicates an adjusted P value of 0.05. Blue dots represent FLiP markers of P-body proteins. b, Fluorescence micrographs showing yeast cells expressing the P-body marker Dcp2 tagged with GFP, with and without exposure to HU. Scale bar, 5 μm. c, Mass spectrometry signal intensities of FLiP markers for selected P-body proteins in control and under HU stress; four replicates are shown. d, The schematic shows selected P-body proteins with the location of several features marked along the protein sequence. Shown are known PBIs (red), FLiP markers (yellow), structural changes on HU stress identified by LiP–MS (blue) and detected but nonchanging peptides (gray). e, Structure of the Pat1–Lsm1-7 complex (PDB 4C8Q, ref. ⁷¹). The FLiP markers significantly changing on HU stress for Lsm5, Lsm6 and Lsm7 are shown in yellow. f, Structure of Asc1 (light gray) in complex with the small ribosomal subunit (dark gray) (PDB 6FAI, ref. ⁷⁴). The FLiP markers significantly changing on HU stress are shown in yellow.