mzML 1.1.0 Specification

From 2005-2008 there has existed two separate XML formats for encoding raw spectrometer output: mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. It was recognized that the existence of two separate formats for essentially the same thing generated confusion and required extra programming effort. Therefore the PSI, with full participation by ISB, has developed a new format by taking the best aspects of each of the precursor formats to form a single one. It is intended to replace the previous two formats. This new format was originally given a working name of dataXML. The final name is mzML.

On 2008-06-01, mzML 1.0.0 was released.

In early 2009, several implementation efforts have identified a few minor shortcomings in mzML 1.0.0. Since no vendors have yet released software supporting mzML 1.0, but have identified a few minor problems with it, the working group has decided to release an update in June 2009. It is expected that all software will support mzML 1.1 as the long-term-stable format instead of 1.0. Below are the available documents and initial implementations. We encourage the community to begin implementing mzML 1.1.0, to phase out use of mzData and mzXML, and to send feedback to psidev-ms-dev@lists.sourceforge.net.

On 2009-06-01, mzML 1.1.0 was released. There are no planned further changes as of early 2013.

 

mzML Release Schedule

(updated 2013-05-02)

  • 2008-06-01 mzML 1.0.0 released
  • 2009-06-01 mzML 1.1.0 released
  • 2010-06-01 mzML index wrapper schema updated to 1.1.1
  • 2013-05      Minor updates to CV still occur, but no new schema changes are planned at this time

 


mzML 1.1.0 Finished Specification

(updated 2010-07-13)

The information and documents in this subsection are related to mzML 1.1.0, revised after going through the PSI document process on May 19, 2009. Everyone is encouraged to update their implementation to mzML 1.1.0 and release software supporting that instead of mzML 1.0. It is sincerely hoped that mzML 1.1 will remain stable for a long time.

NOTE: On 2010-06-01, the mzML index schema was updated from 1.1.0 to 1.1.1. There was no functional change, but rather the addition of an enumeration constraint to an attribute to prevent creative, unintended values. This could cause some files that previously validated to no longer validate. However, any such files should never have successfully validated in the first place.

XML schema definition files:

- mzML1.1.0.xsd (main schema)

- mzML1.1.1_idx.xsd (separate and optional index)

- Latest mapping file, which defines where certain controlled vocabulary terms may be used in a document.

- Latest version of the controlled vocabulary (CV) (from CVS) in OBO 1.2 format. (metadata) (See recent diffs) (OBO-Edit)

Documentation files:

- Full Specification Document: mzML1.1.0_specificationDocument.doc

- HTML schema documentation for mzML 1.1.0

- HTML schema documentation for mzML 1.1.0 index wrapper schema

- ASMS June 2009 Poster (3MB PPT) 

Validation of mzML files

 - mzML semantic validator created by Marc Sturm (OpenMS/TOPP)

 - mzML semantic validator at ProDaC

The OpenMS/TOPP validator can be installed locally by downloading and installing OpenMS. The source code for a Java-based validator is available at SourceForge.

For more information on PSI MS validators, please see the dedicated information page.

Sample instance documents for all relevant formats:

All documents are meant to contain equivalent information in the various formats.

- tiny1.mzML1.1.0.mzML
- tiny1.mzData1.05.xml

- tiny1.mzXML2.0.mzXML
- tiny1.mzXML3.0.mzXML

Sample files generated by the ProteoWizard:

- small.RAW (a small Thermo RAW file with LTQ-FT data)

- small.pwiz.1.1.mzML (converted from small.RAW by msconvert)

- small_miape.pwiz.1.1.mzML (converted by msconvert, with example MIAPE fields added programatically)

- small_zlib.pwiz.1.1.mzML (converted by msconvert, with zlib compression and 32-bit precision)

Sample files generated by the Proteios Software Environment:

A standalone converter package and the original peak lists can be found here.

- dta_example_1.1.0.mzML (generated by conversion of a folder of DTA files)

- plgs_example_1.1.0.mzML (generated by conversion of a Protein Lynx Global Server xml peak list

Hand crafted sample files illustrating different scan types

- neutral_loss_example_1.1.0.mzML (neutral loss scan example)

- precursor_spectrum_example_1.1.0.mzML (precursor scan example)

- MRM_example_1.1.0.mzML (SRM example)

Other sample files:

 - PDA example file (createdby Steffen Neumann)

Other relevant websites:

- psidev Sourceforge site

- PSI mzML CVS

- PSI mzML SVN (currently just the semantic validator code)

- General PSI guidelines for creating controlled vocabularies

- OBO-Edit (a software to explore CV files in OBO format)

 

 Current and future support for mzML:
(updated 2013-02-19)

Product
Source
Contact
 
Support comments
ProteoWizardUSCParag MallickFull mzML support today
TPPISBEric DeutschFull mzML support today (including embedded X!Tandem)
Insilicos ViewerInsilicosErik NilssonFull mzML support today
X!TandemGPMRon BeavisFull mzML support today
MyrimatchVanderbiltMatt ChambersFull mzML support today
InSilicoSpectroSIBAlex MasselotFull mzML support today
Proteios SEUniv LundFredrik LevanderFull mzML support today
NCBI C++ toolkitNCBIDouglas Slottaavailable in next release
OpenMS/TOPPUniv TübingenMarc SturmFull mzML support today
PhenyxGeneBioPierre-Alain BinzFull mzML support today
MascotMatrix ScienceDavid CreasyFull mzML support today
Mascot DistillerMatrix ScienceDavid CreasyFull mzML support today
jmzMLGhent/ EMBL-EBILennart MartensFull mzML support today
Conversion tool in Proteomics ToolboxThermo ScientificJim Shofstahlbeta testing
ReAdW (.RAW converter)ISBEric DeutschReplaced by ProteoWizard msconvert
mzWiff (.wiff converter)ISBEric DeutschReplaced by ProteoWizard msconvert
MassWolf (.raw/ converter)ISBEric DeutschReplaced by ProteoWizard msconvert
Trapper (Agilent data converter)ISBEric DeutschReplaced by ProteoWizard msconvert
mzML_ExporterABISean Seymourbeta testing
CompassXportBruker??
PEAKSBioinformatics Solutions IncKevin ZhangBeta Testing
PRIDE databaseEMBL-EBIJuan A. Vizcainoongoing
PRIDE InspectorEMBL-EBIJuan A. VizcainoFull mzML support today
MIAPE MS ExtractorProteoRedSalvador Martinez-BartolomeFull mzML support today
mzRBioconductorBernd Fischer, Steffen Neumann, Laurent GattoFull mzML support today
pymzMLUniv MünsterChristian FufezanFull mzML support today
CruxUniversity of WashingtonW. NobleFull mzML support

 

 


Released mzML 1.0.0 Specification

(updated 2009-02-10)

The information and documents below related to mzML 1.0.0, which is now obsolete. Do not use it.

Current xml schema definition files (.xsd):

- mzML1.0.0.xsd (main schema)

- mzML1.0.0_idx.xsd (separate and optional index)

Documentation files:

- Full Specification Document: mzML1.0.0_specificationDocument.doc

- HTML schema documentation for mzML 1.0.0

- HTML schema documentation for mzML 1.0.0 index wrapper schema

- ASMS June 2008 Poster (3MB PDF)




Old Stuff:

Old stuff that should be updated!!:

- tiny2_SRM.mzML0.99.1.mzML (hand crafted)

- tiny3-pmf.mzML0.91.xml (not yet updated)

- 1min.0.99.1.mzML (software-generated conversion of Thermo RAW file by ReAdW)

- 2min.0.99.1.mzML (software-generated conversion of MassLynx raw folder by Wolf)

Multiple file kits for mzML:

- mzML_0.99.1.zip: Zip file of most of the above files (350 kB)

- mzML_0.99.1_large.zip: Larger zip file including more sample data and software (12 MB)

- ISB ReAdW converter for Thermo RAW -> mzML beta test kit (0.99.1)

- ISB Wolf converter for Waters raw -> mzML beta test kit (0.99.1)

Minutes and notes from June 2007 conference at EBI

- Minutes from Monday

- Minutes from Tuesday

- Minutes from Wednesday

- To Do items

Minutes and notes from April 2007 conference in Lyon

- Minutes from Monday

- Minutes from Tuesday

- Minutes from Wednesday

- Open Issues Document

- 2007-06-12 Conference call notes


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