The Workspace is divided into two parts: the overview-panel on the left-hand side, and the details-panel on the right hand side.
The details-panel is divided into five sections:
This is the tab that's active when you are reading this, and contains information on how to use this platform, as well as on the underlying experiments and models.
In this tab, detiled plots of the timecourse data for individual peptides are collected.
In this tab, profile views are collected. These are similar to the plots in the card-based view, but are optimised for comparison of sequence similarities, and lack details on the timecourses.
This tab contains a list of all the peptides in the dataset. Click on an entry to produce card and profile of it.
- Connected views
Views relating to peptides are linked: Hovering over a point in the scatterplot, will highlight the corresponding card or profile, if the respective tab is active. Likewise, hovering over a card, profile or entry in the peptide-list will highlight the corresponding point in the dataset.
Searching for peptides
The search bar at the top of the details-panel allows you to search for peptides based on their gene-names or peptide ids. In order to generate a card and profile for a selected entry press enter. If you are searching for gene names, all corresponding matches in the dataset will be plotted.
- Downloading plots
The download icon on cards and profiles allows you to download the corresponding chart as svg. On Safari, this will open a new tab, which displays only the svg. On Chrome and Firefox, the svg should download automatically
- Destroying plots
The destroy button on cards and profiles allows you to remove them from the workspace. Items associated with the same peptide are connected, therefore clicking the destroy button on a card will also remove the associated profile. The button to clear the entire workspace is located in the search bar of the details-panel.
- Look-up on pubmed
This button will open a new tab in your browser and look up the associated protein in the pubmed database.
The overview-panel is designed to provide you with a convenient interface for producing scatterplots of the dataset:
- The two histograms next to the y axis and below the x-axis show the distribution of peptides along the that particular axis. The coloured set of bars correspond to the subset of peptides shown in the scatterplot.
- The scatterplot area
- Zooming You can zoom in on the scatter plot by resizing the grey box overlaid on the histograms.
- Hovering over a datapoint in the scatterplot will show you the id of the corresponding peptide, which is composed of the gene-name, the phosphorylation-site and an indication of whether it was seen in the supernatant or in the pellet-fraction.
- Clicking a datapoint in the scatterplot will produce detailed plots that can be viewed in the details-panel
- Drawing a rectangle on the scatterplot-area will select all points contained within its area and plot detailed plots that are accessible through the details-panel.
This tool works best with the most recent versions of Google Chrome, Firefox and Safari.
Mobile: A mobile-optimised version of this tool is under development