Skip to content

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 1.3.0 (current release)

2. mzIdentML 1.2.0

3. mzIdentML 1.1.1

4. mzIdentML 1.1.0: XML Schema, Documentation and Ontology

5. mzIdentML Tools and Implementations

6. mzIdentML 1.0.0: Schema, documentation and ontology

mzIdentML 1.3.0 (Released June 2024, current release)

PSI-PI has updated mzIdentML from version 1.2 to 1.3. The core of this specification document remains unchanged from 1.2.0, but version 1.3.0 now supports extensions for additional features or use cases, described in additional extension documents located in the same folder. It is important to highlight that extension documents cannot introduce any changes to the mzIdentML schema. As such they are primarily about introducing and describing the use of CV terms.

Small refinements and clarifications have also been added to the main specification document.

In parallel with the mzIdentML 1.3 specification, an extension document has been developed for crosslinking Mass Spectrometry (MS) experiments.

 

mzIdentML 1.2.0 (Released March 2017)

In 2013-2017, PSI-PI 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.

    • Rosetta – Excel file detailing how concepts from different software packages map onto the new guidelines.

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:

    • Conformance with MIAPE is here

    • Conformance with the Molecular and Cellular Proteomics Publication guidelines is here 

    • Example Instance Documents:
        • Mascot MS MS example – a simple example of 4 ms-ms spectra searched against a protein database.

        • 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.