Although the option for partial submissions is available, it isn't recommended as it siginificantly reduces the visablity and reusability of your dataset. You should only use this option if your search results cannot be converted to the PRIDE XML format by using PRIDE Converter or PRIDE Converter 2.
The partial submissions pipeline (Figure 6) requires you to have the raw data (mass spectrometer output files), search engine output files (output from search engine or analysis pipeline) and a PRIDE login, so you will need to register. Your username and password will allow PRIDE to securely process your submission.
Figure 6. ProteomeXchange MS/MS data workflow for partial submissions.
The tool creates appropriate relationships between the different file types used in a partial submission i.e. the raw data and search engine output files.
The PRIDE team is planning to support the standard mzIdentML data format in the near future, so there will be no need to convert your search results to PRIDE XML. However, at the moment only PRIDE XML is fully supported.