Hi Josh, all

thanks for the fast reply...
I've used the file you posted and the requests now get added to the Assay List. (See screenshot)

At the end of the cmdline output (See attachment) we get the error:
'Exception in thread "main" java.lang.reflect.InvocationTargetException'
Caused by: java.lang.IllegalArgumentException: Failed to load requested protocol 'nitro_test_with_fasta_IDX2.xml', it may not exist.

The expected location of the protocol accordong to the MS2SearchClient notes would be T:\LabKeyRoot_v11\v11_Test\@files\.labkey\protocols\sequest\ in our case, I verified the file nitro_test_with_fasta_IDX2.xml does exist there.


I cannot spot where the mistake is, so I zipped all related files and attached them to this posting.
Can you help us here?

Thanks for all, cheers
Jean