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.
- mzIdentML 1.2.0-draft
- mzIdentML 1.1.0 (Current Release Version): XML Schema, Documentation and Ontology
- mzIdentML Tools and Implementations
- mzIdentML 1.0.0 (Previous Version): Schema, documentation and ontology
There is a planned, relatively minor updates to mzIdentML specification, which is likely to complete in 2014. The main update relates to improvement in the representation of protein grouping relationships, through the use of mandatory CV terms. Minor updates are also being proposed for capturing pre-fractionation of samples, de novo sequencing and the use of multiple search engines.
- Draft specification document
- Draft example files
- Rosetta - Excel file detailing how concepts from different software packages map onto the new guidelines
Released in August 2011.
More documentation is available in the PSI PI Google code project at http://code.google.com/p/psi-pi/.
Direct Links to deliverables:
- Specification Document (PDF)
- mzIdentML validators:
- presentation sketching the changes of mzIdentML version 1.1
- 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.
- 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
Current status of tools that write and import mzIdentML are on this page.
This was the first version of the mzIdentML format, released August 2009.
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.
- mzIdentML 1.0.0 Schema (xsd)
- FuGElightv1.0.0.xsd Schema (.xsd)
- Documentation (PDF)
- Documentation (Microsoft Word format)
- Example files