Can I Submit mzIdentML Files from ProteinPilot™ Software 5.x to the PRIDE Repository?

For research use only. Not for use in diagnostic procedures.

Answer

The short answer is no. Submission of mzIdentML files is still not automated with later versions of ProteinPilot™ software. The problem is that the release of ProteinPilot software 5.0 was based on a draft of the mzIdentML 1.2 specification document, and the final mzIdentML 1.2 specification differs significantly from the draft. ProteinPilot 5.0 has not yet been updated to this new specification. For this reason, the automated mzIdentML validation in PRIDE still currently fails for files submitted from ProteinPilot software.

Specifically, the issues the PRIDE repository has with the files from ProteinPilot software are that the raw .wiff files are referenced in the mzIdentML export file, and these cannot be read in the PRIDE viewer. Because of this, complete submissions from ProteinPilot software to PRIDE are not possible, but partial submissions of the mzIdentML are, and this partial submission process is described below. (Note: the vast majority of submissions to PRIDE continue to be partial submissions.)

A partial submission is the only option for automatically submitting mzIdentML files from ProteinPilot software at this time. All the current documentation and access to the ProteomeXchange (PX) submission tool can be found at www.proteomexchange.org/submission and the tutorial is also printed below.

To complete a partial submission to the PRIDE repository, follow these steps:

1. Convert the .group file to the XML format using our Group File Extractor tool, which can be found in the ProteinPilot program files located at C:\Program Files\AB SCIEX\ProteinPilot. This is a command-line tool. 
2. Convert the wiff data file to mzML using the Sciex Data Converter which can be download from our website at https://sciex.com/content/SCIEX/na/us/en/support/software-support/software-downloads.html.
3. Open the PX submission tool and choose the Partial Submission option on the first screen.

The tool does mainly three things:

• Creates links between the raw data and the result files (and potentially others).
• Provides minimal metadata (to be compliant with the PX announcement message also available for fully supported submissions.
• Sends the files to the European Bioinformatics Institute (EBI).

The ProteomeXchange Consortium was established to provide globally coordinated standard data submission and dissemination pipelines involving the main proteomics repositories and to encourage open data policies in the field. The PX announcement messages and PX data submission guidelines can be found here: http://www.proteomexchange.org/.