For research use only. Not for use in diagnostic procedures.
Answer
If you are trying to export ProteinPilot™ software data to the PRoteomics IDEntifications PRIDE database, then the partial submission mechanism is your only option at this time. All the current documentation and access to the ProteomeXchange (PX) submission tool can be found at www.proteomexchange.org/submission.
To submit data to the PRIDE database, data will need to be converted:
- Converting .group files to XML file format. Data from ProteinPilot 4.x software can be converted using group2xml (a command line tool), installed in the C:\Program Files\AB SCIEX\ProteinPilot\ folder. Data from ProteinPilot 5.x can be converted using GroupFileExtractor.exe, located in the C:\Program Files\AB SCIEX\ProteinPilot folder.
- Converting .wiff or TOF/TOF data to mzML. Data can be converted using the AB SCIEX Data Converter (1.3b) can be used (https://sciex.com/software-support/software-downloads).
After converting the data, open the PX submission tool and choose partial submission on the first screen.
The tool does three things:
- Creates links between the raw data and the result files (and potentially others).
- Asks users to provide minimal metadata (to comply with PX announcements that are also available for the fully supported submissions).
- Submits files by FTP to the EBI (European Bioinformatics Institute, www.ebi.ac.uk).
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