Mass Spectrometry

mzIdentML

mzIdentML is one of the standards developed by the Proteomics Informatics working group of the PSI.

For general information of the activities and the organization of this working group see HERE.

Contents

  1. mzIdentML 1.2.0 (current release)
  2. mzIdentML 1.1.1
  3. mzIdentML 1.1.0: XML Schema, Documentation and Ontology
  4. mzIdentML Tools and Implementations
  5. mzIdentML 1.0.0 (Previous Version): Schema, documentation and ontology

 


mzIdentML 1.2.0 (Released March 2017 - current version of the standard)

In 2013-2017, PSI-PI has updated mzIdentML from version 1.1 to 1.2. The main update relates to improvement in the representation of protein grouping relationships, through the use of mandatory CV terms. Minor updates have also being proposed for capturing pre-fractionation of samples, de novo sequencing and the use of multiple search engines. Specifications have also been added for supporting proteogenomics and cross-linking MS.

 


mzIdentML 1.1.1: XML Schema, Documentation

Released in July 2015, as a minor update to version 1.1.0. This update should be viewed as a "bugfix" update only.
The only change is to ensure that mass deltas encoded in the format are consistently encoded as doubles and not as floats. As of March 2017, both mzIdentML 1.1.1 and 1.2 (see above) will be generally supported for some years, although we strongly encourage new implementers to work with mzIdentML 1.2.

This has resulted in a change to the schema (XSD) and the specification document only. All other resources are unchanged from version 1.1.0.

 


mzIdentML 1.1.0: XML Schema, Documentation and Ontology

Released in August 2011.

More documentation is available in the HUPO-PSI GitHub page at https://github.com/HUPO-PSI/mzIdentML.

Direct Links to deliverables:

  • Example Instance Documents:
    • Mascot MS MS example - a simple example of 4 ms-ms spectra searched against a protein database.
    • Mascot Nucleic Acid Example - an example of a search against an EST database
    • Mascot Top Down example - a single ms-ms spectra from a protein.
    • MPC Use case - use peptides from different search engines to assemble proteins with a third-party algorithm;
      false-discovery estimation using decoy database.
    • OMSSA - example MS-MS search results including decoy matches
    • PMF Example - example Peptide Mass Fingerprint search
    • Sequest -a simple example derived from a .out file
    • X! Tandem - example MS-MS search results including decoy matches

 


 

mzIdentML Tools and Implementations

Current status of tools that write and import mzIdentML are on this page.


 


 

mzIdentML 1.0.0 (Previous Version): Schema, documentation and ontology

 This was the first version of the mzIdentML format, released August 2009. mzIdentML 1.0.0 is NOW DEPRECATED - users should use mzIdentML 1.1.x or 1.2 versions.

mzIdentML was developed as an extension to the Functional Genomics Experiment (FuGE) object model. However, in a change agreed at the PSI Spring Meeting, 2008, the XML schema was developed directly rather than performing the design in UML and converting to XML. A cut-down version of the FuGE xsd has been developed to facilitate this. As a consequence, the UML class diagram in subversion is now out of date.

 

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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) in OBO 1.2 format.  (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

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:

 

Hand crafted sample files illustrating different scan types

 

Other sample files:

 - PDA example file (createdby Steffen Neumann)

Other relevant websites:

- HUPO-PSI GitHub mzML

- 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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Mass Spectrometry Workgroup

PSI-MS: Mass Spectrometry Standards Working Group

About us

The PSI-MSS working group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the the field of proteomics mass spectrometry.

 

Current projects are:

  • The mzML format, which merges the mzData format (see below) and another similar format mzXML. mzML 1.1.0 was released on June 1, 2009 and has been stable since then. Everyone is encouraged to implement mzML 1.1.0 in their software. See the mzML information page for the full specification, other documentation and examples.
  • The TraML format has been developed as a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. This specification has been been accepted through the PSI document process and is complete. Please email the list psidev-ms-dev@lists.sourceforge.net with your questions, comments, and suggestions. See the TraML information page for the full specification, other documentation and examples.

Past achievements are:

  • The mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released and is stable at version 1.05. It is now deprecated in favor of mzML.
Note that the mzIndentML (formerly AnalysisXML) format now comes under the aegis of the Proteomics Informatics Working Group.

Group Structure (2009)

Role
 
Name
ChairEric Deutsch, Institute for Systems Biology
Co-chairs

Pierre-Alain Binz, Centre Universitaire Hospitalier Vaudois CHUV

Henry Lam, Hong Kong University of Science and Technology 

Secretary

Andrew Dowsey, University of Bristol 

MIAPEPierre-Alain Binz, Centre Universitaire Hospitalier Vaudois CHUV
Ontology Co-ordinators

Gerhard Mayer, Ruhr-University Bochum 

Other Working Group Members:
 Steffen Neumann, IPB Hall
 Florian Reisinger, European Bioinformatics Institute
 David Creasy, Matrix Science Ltd.
 Wilfred Tang, Applied Biosystems
 Pete Souda, University of California, Los Angeles
 Angel Pizarro, University of Pennsylvania
 Sean Seymour, Applied Biosystems

 

 

mzML Standard 

Status: Released 1.1.0 [more information...]

 

As of 2006 there 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 is recognized that the existence of two separate formats for essentially the same thing generates confusion and extra programming effort. Therefore the PSI, with full participation by ISB, developed a new format intended to replace the previous two formats, by merging the best ideas from each format. This new format is called mzML. See the information page for mzML which includes current documentation, example files and other related materials. We encourage everyone to implement mzML in their software and workflows and cease using mzXML and mzData as soon as possible.

 

Controlled Vocabulary development: The PSI-MS CV
 
The PSI-MS Controlled Vocabulary is developped in common with the PSI-Proteomics Informatics group. It consists of a large collection of structured terms covering description and use of Mass Spectrometry instrumentation as well as Protein Identification and Quantitation software. The source of the terms are multiple: they include vocabulary and definitions in chapter 12 of the IUPAC nomenclature book, instrument and software vendors and developers and other user-submitted terms. Although its structure and use is linked to mzML, mzIdentML and mzQuantML, it is dynamically maintained in a OBO format.
 
The latest version of the PSI-MS CV is available here.
 
To request new CV terms to be added to the PSI-MS Controlled Vocabulary, please use the psidev-vocab mailing list.
 
More information on PSI CVs can be found here.

The mzData standard
Status: version 1.05. Deprecated.

mzData in a nutshell

mzData is a data format capturing peak list information. Its aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into one; mzData. mzData is NOT a substitute for the rawfile formats of the instrument vendors. Some vendors, if not all, will provide software transforming their raw files to mzData. There are already a number of programs which can use mzData. In order to keep the filesize of mzData limited, mz/intensity information is stored in "binary base 64 format".

Technical description and other resources

Questions? Consult the PSI-MS email discussion list

 


Moderated email discussion list

 

We also provide a mail discussion list for mass spectroscopy standard development.
You can mail to this list at psidev-ms-dev@lists.sourceforge.net, or subscribe/unsubscribe.

 


Last edited by: Pierre-Alain Binz 2014-04-09

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TraML 1.0.0 Specification

The HUPO PSI Mass Spectrometry Standards Working Group (MSS WG) has developed a specification for a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. This specification has now completed rigorous review with the PSI document process and is complete. Please email the list psidev-ms-dev@lists.sourceforge.net with your questions, comments, and suggestions.


TraML Development Timeline

(updated 2013-04-22)

  • 2010-03-31 TraML 0.9.4 draft posted
  • 2010-07-01 TraML 0.9.4 submitted as 1.0.0RC1 to PSI document process
  • 2011-08-23 TraML 0.9.5 draft posted
  • 2011-12-12 TraML 1.0.0 released

 


New TraML 1.0.0 Finished Specification

(updated 2013-04-22)

The information and documents in this subsection are related to TraML 1.0.0, now complete in its development cycle. There are currently no open issues for a follow-on version. Everyone is encouraged to examine and implement the formatas widely as possible.

XML schema definition files (.xsd):

- TraML1.0.0.xsd (main schema)

 

Documentation files:

- Full Specification Document: TraML1.0.0.0_specificationDocument.pdf

- HTML schema documentation for TraML1.0.0

- Please cite this journal article when referencing TraML: Deutsch et al. 2011, MCP, 10, R111.015040

 

Controlled Vocabulary and Mapping Files:

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

- Latest development version of the CV in OBO 1.2 format

    You can explore the CV at the NCBO BioPortal, or at the EBI OLS (Ontology Lookup Service), or with the Java desktop application OBO-Edit.

 

Sample instance documents for all relevant formats:

- ToyExample1.TraML

- Yeast_ATAQS_gen.TraML (6 MB)

- Yeast_InclusionList.TraML

 - xcmsIncludeTest.TraML

 - TSQ_1832_jTraML_converted.TraML
 

 

Other resources:

 - On-line TraML converter using Compomics jTraML (current at version 1.0.0)

 - On-line TraML validator at OpenMS (current at version 1.0.0)

 

 

 

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