[Psidev-ms-dev] mzML consistency miscellanea

[Kessner, D. E. <Dar...@cs...>]

Hi all,

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I've collected some notes regarding the mzML spec:

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1)       There are references in the specification document to
InstrumentType, SampleType, etc. that I assume mean <instrument>
element, <sample> element, etc, though this is not explicitly stated
anywhere.

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2)       The <precursor> element has a spectrumRef attribute that is
supposed to refer to the id attribute of a <spectrum>.  However, the
<precursor> element in tiny1.mzML0.99.1.mzML appears to refer to a
scanNumber, not id.  Which is the intended attribute to reference (I
assume 'id')?

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3)       The <cv> element has the attribute fullName=3D"Proteomics
Standards Initiative Mass Spectrometry Ontology".  This text does not
appear in psi-ms.obo - perhaps it should?  Basically, I think it would
be useful to have some identifier that appears in both psi-ms.obo and in
mzML files generated with that psi-ms.obo.  Or even better, an id and a
version, just like the <softwareParam> elements, but in the psi-ms.obo
it could appear in the header.

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4)       Regarding <softwareParam> elements, is there a reason not to
use two of the more general <cvParam> elements, one to specify the
software, and one to specify the version?

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5)   Element reference naming consistency -- in many cases, there is an
element name and a corresponding (either attribute or element) name for
a reference to it:

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<instrument>   <--  instrumentRef

<sourceFile>   <--  sourceFileRef

<spectrum>    <-- spectrumRef

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But there are a few exceptions:

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<referenceableParamGroup>  <-- paramGroupRef=20

<software> <-- softwareRef AND instrumentSoftwareRef

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Suggestions:

Replace <referenceableParamGroup> with <paramGroup>

Remove <instrumentSoftwareRef> and use <softwareRef>

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Since the id attribute is usually used for references, we could also
have:

  <cv id=3D"MS" ... >

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  <cvParam cvRef=3D"MS" ...>

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There is also some redundancy in the naming of <sourceFile> attributes:

<sourceFile id=3D"1" sourceFileName=3D"tiny1.RAW"
sourceFileLocation=3D"file://F:/data/Exp01" >

could be shortened to:

<sourceFile id=3D"1" name=3D"tiny1.RAW" location=3D"file://F:/data/Exp01"=
 >

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Darren

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Darren Kessner

Scientific Programmer

Dar...@cs...

310-423-9538

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Spielberg Family Center for Applied Proteomics

Cedars-Sinai Medical Center

http://www.sfcap.cshs.org/

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