Sharing proteomics data or reusing proteomics data in other context is getting more and more common. It is then important to have standard formats to ensure that the data can be read and understood, and one of the standard formats is mzIdentML.
PeptideShaker's built in mzIdentML export function makes it straightforward to convert all the protein identifications in your experiment to the mzIdentML format. All you need to do is to add some additional information about your project, the converter takes care of the rest.
Keep in mind that the current PeptideShaker settings are used when
converting the project.
Make sure that all settings (like the annotation
level and the fragment ion accuracy) is set to the desired values before
starting the conversion!
All files created by the built in mzIdentML exporter should be valid and supported
in all tools using mzIdentML, but if you do come across any issues, please do not hesitate to let us know.
See http://compomics.github.io/projects/peptide-shaker.html
for how to contact us.