The data in this repository are associated with the manuscript Towards designer organelles by subverting the peroxisomal import pathway Laura L. Cross, Rupesh Paudyal, Yasuko Kamisugi, Alan Berry, Andrew C. Cuming, Alison Baker & Stuart L. Warriner Nature Communications 2017 The manuscript employs screening of a variety of mutants of the protein PEX5 against a library of peptides using a pull down assay, analyzing which peptides are retained by LC-MS analysis. The MS files contain data for each mutant and comprise raw data files (Bruker), pdfs of extracted ion chromatograms which are then processed using the retention time information (contained in manuscript SI) to identify which peptides are pulled down. These data are then plotted in heat map form (Origin). The MS data are divided into the most interesting set (presented in the manuscript) and the other data presented in the SI. The FAresults.csv contains raw data used to create the Fluoresence anisotropy curves. The second part of this project involved analyzing intracellular distribution of red and green fluorescent proteins by fluorescence and confocal microscopy in czi format which can be read with ImageJ or other microscopy software. Images in the MicroscopyImages.zip archive should be interpreted in conjunction with the data in Supplementary Data 3. The confocal Images.zip archive contains raw data for the images presented in the manuscript. The PEX11 mutant data contains image data for the corresponding Supplementary Figure