Fix for pepXML loading bug (#710)

Small fix and update of a test case (for the IDFileConverter TOPP tool).
The cause of the bug: The variable that was intended to store whether the requested experiment had been found in the pepXML file was reset for every experiment encountered - so it would only work if the requested experiment was the last one.
For the test, I've added an "msms_run_summary" with a different "base_name" (different experiment) to the file, which would have triggered the bug/error before the fix.

fixes #710