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Several changes to support Proteome Discoverer version 3.1 and the new MS Amanda engine
Bugfixes:
Introduced a consistency check for decoy protein order that should prevent debug prompts for "not all accessions found in target and decoy files"
Additional notes: This version of MS Annika 2.0 only works for Proteome Discoverer 3.1.0.395. The current release version of Proteome Discover (3.1.0.638) requires MS Annika 2.0 v2.2.2!