How can I use the Encyclopedia of Proteome Dynamics (EPD) to view HipSci data?

All the resulting HipSci raw MS data are available for download from the PRIDE repository. In addition, the corresponding processed MS data can be accessed via the Encyclopedia of Proteome Dynamics (EPD), which has a section dedicated to HipSci data. This is a rapidly developing resource and is regularly updated with new data, new interactive features and further integration of the proteome data with other HipSci data sets from both normal and disease cell lines.

These data can be accessed as follows:

  • Navigate to peptracker.com/epd
  • Enter Proteins dynamics viewer
  • On the graphical interface click on the circle labelled ‘Stem Cells’
  • After Stem Cells is selected, the interactive navigation will update itself and display a bubble labelled ‘HipSci’.
  • Click on the HipSci bubble to explore data available for the project.
  • Selecting HipSci will show you two red circles, representing interactive visualisations that can be accessed when clicked upon.

  • The red circles represent interactive visualisations made specifically for the HipSci project.
  • Clicking on the icon with circles of varying size will open a bubble plot.
  • This plot shows the abundance measurements for every single protein that was detected for every HipSci line.
  • There are two dropdown menus that you can interact with:
    • The first displays either protein abundance, or protein abundance transformed to a log 10 scale, across all HipSci cell lines.
    • The second drop down lets you select specific HipSci cell lines and will draw a new bubble plot showing protein abundance in the selected cell line.
  • Clicking on the circle with the image of a bar plot will open a histogram:
    • The first histogram shows the abundance distribution on a log 10 scale
    • This plot also has a dropdown that allows for a selection of a specific HipSci cell line

Additionally, the EPD allows users to search for specific proteins of interest, based on uniprot protein IDs, which displays results that highlight data for the selected protein in the HipSci cell lines. The navigation pane has a text box labelled ‘Protein Search’, as displayed below.

You can search for proteins based on either a description, gene, name or Uniprot accession. When you have selected a protein of interest this will modify the output you receive from the interactive plots.

  • The Bubble plots will adapt to show you the abundance of the specific protein of interest across all HipSci cell lines where that protein has been detected.
  • The histogram will highlight in red the abundance bin where the protein of interest is located.