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Issue on library in Peptide setting hogeun kwak  2021-12-08 02:34
 

Dear Skyline team,

Hello, my name is Hogeun.
I am testing the prm-PASEF using skyline-daily(21.1.9.335).
We took our PASEF data including Ion Mobility using timsTOF Pro 2.
And the characterized DDA file was extracted from PEAKS (Xpro).
I found the attached message when I input the .pep.xml (including IM data from PEAKS) in library option in Peptide setting .
Do you know the reason? Could you give me the solution if you know that?

best regards,

Hogeun Kwak
 
 
Matt Chambers responded:  2021-12-08 10:26
This is an mzXML reading error. Whatever tool created your mzXML needs to fix their writer. The only valid values are RAWData and processedData. From the mzXML 3.2 schema:

<xs:attribute name="fileType" use="required">
<xs:annotation>
<xs:documentation>Was the parent file a native acquisition file? Or was it processed data?</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="RAWData"/>
<xs:enumeration value="processedData"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>

You can work around this by editing that attribute and changing it to processedData. You may run into another error after that though. Honestly this should probably be a warning in ProteoWizard rather than a fatal error. We don't use that attribute's value for anything.