Re: [Psidev-ms-dev] Minor spec doc comment

[Eric D. <ede...@sy...>]

Hi Andy, thanks for this, I have updated references of AnalysisXML to
mzIdentML. As far as the relationship to other specs, I thought it would be
nice to maintain some reference to the other related formats like spML,
since it inevitably comes up every year why mzML doesn't contain something
so important as chromatography information. Here's what it currently says:

 

 

1.      MIAPE MS (http://www.psidev.info/index.php?q=node/91) The "Minimum
Information About a Proteomics Experiment: Mass Spectrometry" module
document identifies the minimum information required to report the use of a
mass spectrometer in a proteomics experiment. The mzML format has been
designed to encode the requirements specified in MIAPE MS. However, mzML
does not enforce MIAPE compliance itself; mzML documents may be valid and
useful without being fully MIAPE compliant. The mzML validator has settings
to validate at either the basic mzML level or at a MIAPE MS compliant level,
depending on the needs of the user.

2.      spML (http://www.psidev.info/index.php?q=node/90). spML (sample
processing Markup Language) is the proposed PSI standard for describing
general protein separation and sample processing other than gel
electrophoresis. GelML is being developed separately from spML because there
is a well defined community associated with gel electrophoresis. As both
GelML and spML build on FuGE (Functional Genomics Experiment) (Jones, Miller
et al. 2007) and use FuGE to describe the relationships between steps in a
proteomics workflow, they will be designed to be straightforward to use
together where appropriate. This document does not assume familiarity with
spML.

3.      mzIdentML (http://www.psidev.info/index.php?q=node/85). The
mzIdentML specification is being developed by the PSI as a standard to
capture the output of search engines that assign mass spectra to protein or
peptide sequences. It is FuGE-based and will provide a UML model as well as
an XML schema. It is anticipated that mzML will serve as an important
'input' to the model defined by mzIdentML. This document does not assume
familiarity with mzIdentML or FuGE.

 

Does that seem good?

 

Thanks,

Eric

 

 

 

 

 

> -----Original Message-----

> From: Jones, Andy [mailto:And...@li...]

> Sent: Thursday, May 21, 2009 8:24 AM

> To: 'Mass spectrometry standard development'

> Subject: [Psidev-ms-dev] Minor spec doc comment

> 

> Hi all,

> 

> I noticed a minor error in the mzML spec doc:

> 

> 2.2  Relationship to Other Specifications

> 

> I think this section was copied and pasted from the GelML specification so

> doesn't make a lot of sense - I would remove sub-sections 2-4. Could you

> also change subsection 5 from analysisXML to mzIdentML if this isn't too

> late for changes ;-)

> 

> Cheers

> Andy

> 

> 

> 

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