MSConvert: mzXML dataProcessing elements fail schema validation

[proteowizard]

MSConvert: mzXML dataProcessing elements fail schema validation

[austinkeller]

Looking at the mzML schema, the dataProcessing group is separated into a softwareList and dataProcessingList. Here is the output from performing identical conversion as above except to mzML instead of mzXML:

     <softwareList count="2">
      <software id="Xcalibur" version="2.8-280502/2.8.1.2806">
        <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
      </software>
      <software id="pwiz" version="3.0.18342">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
    </softwareList>
    <dataProcessingList count="1">
      <dataProcessing id="pwiz_Reader_Thermo_conversion">
        <processingMethod order="0" softwareRef="pwiz">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
        <processingMethod order="1" softwareRef="pwiz">
          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
          <userParam name="Thermo/Xcalibur peak picking"/>
        </processingMethod>
      </dataProcessing>
    </dataProcessingList>

Each processingMethod has a softwareRef. Because mzXML doesn't use references, we'll have to use copies of software elements to represent the same information.

It seems like we'll need to split each dataProcessing sequence used in mzML into a set of separate dataProcessing elements in mzXML to keep with the latest schemas.

[austinkeller]

Resolved by pull request #390