Contexts are a central notion in hEIDI. Basically a context contains an identification result : groups of proteins identified by groups of peptides. This definition can be equally used for identification results issued from a search engine such as Mascot for example as well as identification results build up from many other identifications results compiled together. hEIDI distinguish two types of context :

• a Search context wich is a context associated with the identification result issued from a single search in Mascot (or other search engine). Each time a new search engine result is saved in the database by IRMa, a new search context is created.
• a User context is created by the user in order to organize and aggregate multiple search and/or user contexts.

After having opened an MSI session in your project, you can retreive the User context and Search context hierarchy in the MSIExplorer view.

In hEIDI, a User context is represented with .
A User context contains either other User contexts (child contexts) or identification results, but you can't have both under the same context.

The reason for gathering together several identifications under the same context depends on the user's problematic. Here are some examples:

• Same biological origin
• Same gel
• Same culture conditions
• Same column chromatography
• …

In hEIDI, a Search Context is represented with .