Repository for mzIdentML and the corresponding examples
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germa release/2018-08-09 (version 1.1.6):
renamed and further structured cross-linker related PTMs --> cross-linker related chemical modifications
Latest commit d0cc620 Aug 9, 2018

mzIdentML - Reporting Identifications in MS-based Proteomics Experiments


A large number of different proteomics search engines are available that produce output in a variety of different formats. It is intended that mzIdentML will provide a common format for the export of identification results from any search engine, as well as an import format for post-processing software and public databases.

Citing mzIdentML

When you use mzIdentML format, please cite the following publications:

mzIdentML v1.2: Vizcaino, J. A., Mayer, G., Perkins, S. R., Barsnes, H., Vaudel, M., Perez-Riverol, Y., Ternent, T., Uszkoreit, J., Eisenacher, M., Fischer, L., Rappsilber, J., Netz, E., Walzer, M., Kohlbacher, O., Leitner, A., Chalkley, R. J., Ghali, F., Martinez-Bartolome, S., Deutsch, E. W., and Jones, A. R. (2017) The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & cellular proteomics, mcp.M117.068429 [pdf] (

mzIdentML v1.1: Jones A.R., Eisenacher M., Mayer G., Kohlbacher O., Siepen J., Hubbard S.J., Selley J.N., Searle B.C., Shofstahl J., Seymour S.L., Julian R., Binz P.A., Deutsch E.W., Hermjakob H., Reisinger F., Griss J., Vizcaíno J.A., Chambers M., Pizarro A., Creasy D. The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics. 2012 Jul;11(7):M111.014381 pdf

Specification documents

Version 1.2.0 (April 2017) - Current version:

Specification document

Specification document docx,


Validator (Java) (

Version 1.1.0 (June 2014) - Still supported:

Specification document docx,

The 20 minute guide to mzIdentML docx

Example Files

Several example of the format can be download from the next link Examples

Tools, Libraries, readers and exporters - see (