One solution to this is to use the indexing option ("-o T") in
formatdb when formatting your BLAST database for OMSSA searching. In
my experience, that will result in OMSSA writing the first word of the
protein definition line to the "protein" attribute in the pepXML.
Without the -o option, OMSSA just puts a number in the "protein="
attribute indicating that the hit came from the nth entry in the
database.
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