Label-Free Quantitative Proteomics Data for NPC Permeability Barrier Dynamics

This dataset contains label-free quantitative (LFQ) mass spectrometry analyses of proteins associated with affinity-purified isolated native Saccharomyces cerevisiae nuclear pore complexes (NPCs). The study compared wild type NPCs (+CP WT NPCs) with NPCs frozen at -80°C, or incubate in buffer at 4°C for the indicated days, which led to loss of the central plug (−CP WT NPCs). +CP WT NPCs were also compared to NPCs obtained from mutant strains where nearly half of the mass of FG repeats have been deleted (ΔFG), or increased by doubling the size of the FG region of Nsp1 (Nsp1FGx2). LFQ analyses indicated that the presence of the central plug is strongly associated with a persistent fraction of karyopherins (Kaps) and other factors residing within the NPC. In contrast, the quantities of other NPC components remained stable within the precision of the method for WT and mutant NPCs.