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ProteinLynx Global Server does not process DDA data - WKB21428

Article number: 21428
This article is a portion of a Troubleshooting Path.  To see links to other articles related to MassLynx data dependent acquisition (DDA) , please select the link below.
MassLynx data dependent acquisition (DDA) questions
Articles containing tips on setting up MassLynx DDA methods, solutions and known workarounds to problems with DDA in MassLynx, answers to DDA questions, and corrections to outdated DDA information in MassLynx Help files
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  • After processing DDA data, there are no results
  • Processing of MSe data works fine
  • If the search step (workflow) uses the Mascot search engine, the Mascot server returns error code M00390: "Too many peptide masses in your data file or queries without any ions. Mascot has a limit of 1000 for PMF search. Probably wrong type of search or wrong input format."


  • PLGS 3.0.3
  • PLGS 3.0.2
  • PLGS 3.0.1
  • PLGS 3.0
  • PLGS search engine
  • Mascot search engine


The wrong workflow search type was selected. You must use Fragment Ion Search.

The Mascot error described in the symptoms section results from using the Peptide Mass Fingerprint option in PLGS Workflow > database search.


Select Fragment Ion Search (FIS) as the workflow search type for DDA experiments:



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