metaspace2020 / metaspace

Cloud engine and platform for metabolite annotation for imaging mass spectrometry
https://metaspace2020.eu/
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Dataset with 64-bit intensities has binary ion images #482

Closed intsco closed 4 years ago

intsco commented 4 years ago

https://metaspace2020.eu/annotations?db=NPA-2019-08&ds=2019-11-18_12h37m23s

LachlanStuart commented 4 years ago

Another dataset appeared with this problem from a different user: 2019-04-25_16h19m44s (private)

Both imzML files had the following metadata:

  <softwareList count="2">
    <software id="Xcalibur" version="2.2">
      <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
    </software>
    <software id="TMC" version="1.1 beta">
      <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
    </software>
  </softwareList>
  <dataProcessingList count="2">
    <dataProcessing id="XcaliburProcessing">
      <processingMethod order="1" softwareRef="Xcalibur">
        <cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal" value=""/>
      </processingMethod>
    </dataProcessing>
    <dataProcessing id="TMCConversion">
      <processingMethod order="2" softwareRef="TMC">
        <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
      </processingMethod>
    </dataProcessing>
  </dataProcessingList>

However, checking the other imzML files I have on hand, there are plenty of error-free imzML files that have the same versions of Xcalibur and TMC.

The only common thread - both of these datasets use 64-bit intensity values. All other Xcalibur v2.2 datasets that I have use 32-bit intensity values.