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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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nameValue in mzXML confusing mzR #213

Open sneumann opened 4 years ago

sneumann commented 4 years ago

Hi, in issue #206 two issues were intermingled. @Francisco-madrid-gambin reported on [Serializer_mzXML::Handler_dataProcessing] Unexpected element name: nameValue when opening the file ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS414/1_0a.mzXML due to the line <nameValue name="recalibrationTime" value=""/>

library(mzR)
ms <- openMSfile("1_0a.mzXML")

I get the same error using plain pwiz tools msconvert 1_0a.mzXML -o s (I only checked the rather ancient version 3.0.10827 (2017-5-11)).

processing file: 1_0a.mzXML
[Serializer_mzXML::Handler_dataProcessing] Unexpected element name: nameValue
Error processing file 1_0a.mzXML

As a workaround I can currently only recommend to use the mzR backend "Ramp":

> ms <- openMSfile("1_0a.mzXML", backend="Ramp")
> ms
Mass Spectrometry file handle.
Filename:  1_0a.mzXML 
Number of scans:  3567

Yours, Steffen

sneumann commented 4 years ago

Ok, also happening with 3.0.18342-2. So updating pwiz inside mzR will not help.

I also checked the XML file:

xmllint --schema mzXML_idx_2.1.xsd 1_0a.mzXML 
1_0a.mzXML:16: element software: Schemas validity error : Element '{http://sashimi.sourceforge.net/schema_revision/mzXML_2.1}software': This element is not expected. Expected is ( {http://sashimi.sourceforge.net/schema_revision/mzXML_2.1}processingOperation ).

which shows that the file is not entirely compliant, although not directly related to the error message regarding nameValue. Yours, Steffen