[imzml] KeyError: 'Spectrum Representation'

ISA-tools / mzml2isa

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure

GNU General Public License v3.0

12 stars 6 forks source link

[imzml] KeyError: 'Spectrum Representation' #21

Closed lomereiter closed 7 years ago

lomereiter commented 7 years ago

Lots of imzML files we have don't contain this field in the top-level fileContent node. There are similar entries in IMS ontology that seem to be used more often: IMS:1000030/IMS:1000031

(updated the description)

rsalek commented 7 years ago

Thanks, Artem

@althonos @Tomnl was this to keep the compatibility to mzML2ISA?

http://www.rubydoc.info/search/gems/imzml/0.1.4?q=Spectrum http://www.rubydoc.info/gems/imzml/0.1.4/ImzML/OBO/IMS

proccaserra commented 7 years ago

Any plans for making the vocabulary available from OLS or other ontology server? I could only find it from the following link: https://ms-imaging.org/wp/wp-content/uploads/2016/09/imagingMS.zip thx

Tomnl commented 7 years ago

Thanks @lomereiter,

Is it possible to provide a link to an example imzML file where this has occurred?

lomereiter commented 7 years ago

Some observations on files produced by different converters:

Xcalibur → TMC (standard Thermo software) reports both spectrum representation (profile/centroided) and IBD binary type (continuous/processed) in fileContent
SCiLS Lab (standard Bruker software) reports IBD binary type in fileContent and spectrum representation in the referenceableParamGroup with id "spectrum"
Xcalibur → ProteoWizard → imzmlConverter reports IBD binary type in fileContent and spectrum representation in each spectrum separately

In practice, continuous is pretty much equivalent to profile (because spectra share the same m/z axis) and processed to centroided, but these are different concepts nevertheless.

Attached are examples for the last two conversion scenarios.

example_scils_imzml.zip example_xcalibur_pwiz_imzmlconverter.zip

Tomnl commented 7 years ago

Thanks for the useful information @lomereiter,

At the moment we have been relying on the "Spectrum representation" being in the file content section of the mzML or imzML file.

However, it seems quite often the "spectrum representation" is not recorded here. This actually seems to match up with the mzML schema, where the "spectrum representation" MAY be found in the section but MUST be found in the spectrum section. See cvParam Mapping Rules.

I will look into this

Tomnl commented 7 years ago

Hi @lomereiter, if you could test you get the expected results using this branch.

Tomnl commented 7 years ago

Hi all,

I will close this issue today unless anybody has any objections