Update doc to use new PeptideIdentificationList

[timosachsenberg]

What is the type of your request?
On the C++ side we introduced a class PeptideIdentificationList to encapsulate the vector

In pyOpenMS we previously used pep_ids = [], and then something like IdXMLFile(..., pep_ids) to load the data.

With the new class such code needs to be updated to pep_ids = PeptideIdentificationList()

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Do you have any suggestions for how we can improve the documentation?

[matteopilz]

It looks like this is not used at all, except for in the views folder.

[timosachsenberg]

it is also used in several other places... check the pxd file for the changes to PeptideIdentificationList and trace down if these classes / methods are used in the pyopenms doc and snippets