More and more journals are requesting that you make your proteomics data available when publishing a proteomics manuscript. The most commonly used database for proteomics identifications is the Proteomics Identifications Database (PRIDE).
PeptideShaker's built in PRIDE export function makes it straightforward to convert all the protein identifications in your experiment to the format supported by PRIDE. All you need to do is to add some additional information about your project, i.e., the sample, protocol and instrument used, plus some contact information. The converter takes care of the rest.
The result of the conversion process is a PRIDE XML file. This file can be directly submitted to PRIDE, but we always recommend that you verify the file first using PRIDE Inspector. PRIDE Inspector allows you to see how your data will be presented in PRIDE, and this is your chance to verify that it contains the information you wanted.
For help on how to submit data to PRIDE, please see Submitting your data to PRIDE.
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 PRIDE exporter should be compatible with
PRIDE Inspector (and thus PRIDE), 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.