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IQ-X mzML files cannot be read

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IQ-X mzML files cannot be read Yasin  2025-05-04 05:33
 

Hello,

IQ-X mzML files converted via MSconvert (3.0.25120-02fc3ac) can not be loaded and give the error:
"
At 2:28 PM:
Failed importing results file 'C:\PostDoc\Project_MetallPreliminary\Yasin\Metalls_in_Mushrooms\after_capillary_replacement\mzML\BB.mzML'.
[pwiz::CLI::msdata::ReaderList::read] Invalid cvParam accession "1003411"
"

looking into the file the accession looks like this:

  <referenceableParamGroup id="CommonInstrumentParams">
    <cvParam cvRef="MS" accession="MS:1003411" name="Orbitrap IQ-X" value=""/>
    <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="FSN50178"/>
  </referenceableParamGroup>

Thank you for maintaining the software!
 
 
Matt Chambers responded:  2025-05-06 12:24

Hi, what version of Skyline are you trying to import the mzML with? It might need to be a Skyline-daily for the IQ-X, support for which was only added last October in ProteoWizard (so only a Skyline release after that would have support for the instrument).