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Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
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MaxQuant "StartIndex cannot be less than zero" during `Assemble_run_info` for FAIMS mzXML #639

Closed eschen42 closed 2 years ago

eschen42 commented 2 years ago

We have FAIMS data converted to mzXML with FAIMS-MzXML-Generator.

When we attempt to run the maxquant_mqpar tool Assemble_run_info dies with "StartIndex cannot be less than zero" in Assemble_run_info ####.error.txt. I have attached an example mqpar.xml where only the paths have been changed to protect the innocent.
job_727840_mqpar.zip

Any suggestions for how to proceed?

attn: @npinter

eschen42 commented 2 years ago

@npinter I found that the format of mzXML needs to be MaxQuant compatible. It turns out that FAIMS-MzXML-Generator does not wrote a valid indexOffset node. I was able to overcome this by running openms_fileconverter (which has a maxquant-compatible output mode) after FAIMS-MzXML-Generator; perhaps this could also be achieved using msconvert although I have not proven that to be the case, although its output could be opened by https://github.com/JurgenCox/compbio-base/tree/c6887a64b4563091feef554b18922567275e29d9/PluginRawMzXml

Thus, I am closing this issue.