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 email@example.com.
On 2009-06-01, mzML 1.1.0 was released. There are no planned further changes as of early 2013.
mzML Release Schedule
- 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
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:
- Latest mapping file, which defines where certain controlled vocabulary terms may be used in a document.
- ASMS June 2009 Poster (3MB PPT)
Validation of mzML files
- mzML semantic validator at ProDaC
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.
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:
- PSI mzML SVN (currently just the semantic validator code)
- OBO-Edit (a software to explore CV files in OBO format)
Current and future support for mzML:
|ProteoWizard||USC||Parag Mallick||Full mzML support today|
|TPP||ISB||Eric Deutsch||Full mzML support today (including embedded X!Tandem)|
|Insilicos Viewer||Insilicos||Erik Nilsson||Full mzML support today|
|X!Tandem||GPM||Ron Beavis||Full mzML support today|
|Myrimatch||Vanderbilt||Matt Chambers||Full mzML support today|
|InSilicoSpectro||SIB||Alex Masselot||Full mzML support today|
|Univ Lund||Fredrik Levander||Full mzML support today|
|NCBI C++ toolkit||NCBI||Douglas Slotta||available in next release|
|OpenMS/TOPP||Univ Tübingen||Marc Sturm||Full mzML support today|
|Phenyx||GeneBio||Pierre-Alain Binz||Full mzML support today|
|Mascot||Matrix Science||David Creasy||Full mzML support today|
|Mascot Distiller||Matrix Science||David Creasy||Full mzML support today|
|jmzML||Ghent/ EMBL-EBI||Lennart Martens||Full mzML support today|
|Conversion tool in Proteomics Toolbox||Thermo Scientific||Jim Shofstahl||beta testing|
|ReAdW (.RAW converter)||ISB||Eric Deutsch||Replaced by ProteoWizard msconvert|
|mzWiff (.wiff converter)||ISB||Eric Deutsch||Replaced by ProteoWizard msconvert|
|MassWolf (.raw/ converter)||ISB||Eric Deutsch||Replaced by ProteoWizard msconvert|
|Trapper (Agilent data converter)||ISB||Eric Deutsch||Replaced by ProteoWizard msconvert|
|mzML_Exporter||ABI||Sean Seymour||beta testing|
|PEAKS||Bioinformatics Solutions Inc||Kevin Zhang||Beta Testing|
|PRIDE database||EMBL-EBI||Juan A. Vizcaino||ongoing|
|PRIDE Inspector||EMBL-EBI||Juan A. Vizcaino||Full mzML support today|
|MIAPE MS Extractor||ProteoRed||Salvador Martinez-Bartolome||Full mzML support today|
|mzR||Bioconductor||Bernd Fischer, Steffen Neumann, Laurent Gatto||Full mzML support today|
|pymzML||Univ Münster||Christian Fufezan||Full mzML support today|
Released mzML 1.0.0 Specification
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):
- ASMS June 2008 Poster (3MB PDF)
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)