
mzML beta 1 kit (mzML 0.93 2007-08-01)

This kit contains the latest information, schema, examples for mzML. It is
intended for initial review by major stakeholders prior to submission to
the PSI document process on 2007-09-01.

This kit contains:

README                       - This file, describing the kit
ToDo_stuff.txt               - Notes on still-to-be-addressed items

mzML0.93.xsd                 - mzML schema
mzML0.93_idx.xsd             - mzML index wrapper schema
psi-ms.obo                   - Controlled vocabulary in OBO format

tiny1.mzML0.93.xml           - Tiny hand-crafted two spectrum MS1 + MS2 LCQ example
tiny1.mzData1.05.xml         - Approx equivalent in mzData format
tiny1.mzXML2.0.mzXML         - Approx equivalent in mzXML 2.0 format
tiny1.mzXML3.0.mzXML         - Approx equivalent in mzXML 3.0 format

tiny2_SRM.mzML0.93.xml       - Hand-crafted example of SRM
tiny4_LTQ-FT.mzML0.93.xml    - Hand-crafted example of describing hybrid instrument

1min.mzML                    - Example output of ReAdW Thermo -> mzML converter
2min.mzML                    - Example output of wolf Waters -> mzML converter

validateMzML.pl              - Trivial Perl program to use Xerces to validate a file
mzMLContentHandler.pm        - Reader class used by validateMzML.pl

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Example of the validator (requires Perl with Xerces installed)

./validateMzML.pl --verbose 1 tiny1.mzML0.93.xml
./validateMzML.pl --verbose 1 tiny2_SRM.mzML0.93.xml
./validateMzML.pl --verbose 1 tiny4_LTQ-FT.mzML0.93.xml
./validateMzML.pl --verbose 1 1min.mzML
./validateMzML.pl --verbose 1 2min.mzML

Note that this is a trivial validator. A far more complete semantic validator
is being developed and will be available in August 2007.  It will enforce
proper use of the controlled vocabulary and other rules not enforceable
with XML schema itself.

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Current full kits for converters:

http://tools.proteomecenter.org/software/mzMLKit/mzMLKit-Thermo.zip
http://tools.proteomecenter.org/software/mzMLKit/mzMLKit-Waters.zip

This includes current state of converters including some sample data
to convert. These converters work only on Windows since they use
the vendor libraries, which are provided only for Windows.

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Development web page with additional materials:
http://psidev.info/index.php?q=node/257

Please send feedback to:
psidev-ms-dev@lists.sourceforge.net





