Performing a digest

Step1

Start by entering a name to describe your experiment i.e. Experiment 1. Then search for a gene/protein and select one of the returned matche

View the Screenshot for more details

Step2

Select the sites that you would like the experiment to focus on. You can do this by clicking on the buttons that represent the amino acids.

To deselect a site, simply click it again, or click the 'x' in the table

To automatically select phosphorylation sites for human/mouse, click the button in the top right corner.

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Step3

This step lets you specify the inclusion criterion for peptides that are produced during the simulation. You can control their length, and you can exclude peptides that contain certain unwanted amino acids.

If you select the 'remove cleavages next to phosphorylation sites' option, then cleavage sites next to any of you're selected site will be ignored.

If you select the 'only include results with all specified sites' option, then you will only be presented with enzymes that can produce peptides containing all of your sites.

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Results

Once the simulation has run, you will be presented with the results. The results have an overview pane that outlines the enzymes that can produce peptides with the targeted sites. The details pane gives more detail on each of the peptides that were produced.

The detailed pane also allows you to specify which results to include in the export retports

View the Overview Screenshot and the Peptide Details Screenshot for more details

Combining Results

You can combine the resutls from multiple experiments to identify the best enzyme to use in high throughput experiments View the Screenshot for more details