Submission to ProteomeXchange

ProteomeXchange submission tool

The PX submission tool is a stand alone desktop application that handles both complete and partial MS/MS proteomics submissions to ProteomeXchange (Figure 7). This tool will guide you through the whole submission process.

To run the tool, choose the download option directly from the ProteomeXchange submission tool page.

Figure 7 The PX submission tool setup page gives a download link.

Create a PRIDE account

To start your submission, you will be prompted to enter details for a PRIDE user account. If you haven't already done so, you will need to create a new PRIDE account (Figure 8):

Figure 8 The PRIDE user account registration page.

Creating a PRIDE account is free and only takes a few minutes to register. You should receive an automated confirmation email more-or-less straight away and be able to use your new account. Please contact us by pride-support [at] (email) if your login information is not valid after 24 hours following registration.

Select your workflow

When you launch the ProteomeXchange submission tool, you will be prompted to choose between complete submission and partial submission (Figure 9).

Figure 9 The ProteomeXchange submission tool's welcome screen.

You can choose between two main submission types depending on the availability of mzIdentML or PRIDE XML files as "Result" files for complete submissions. The recommended submission subtype is a complete submission, but alternatively partial submissions are accepted as well. For details about this, please see the PRIDE Help Submission section.

Add your files

On the 'Add files' screen, select all the files you wish to submit and choose which file type they belong to (Figure 12). The tool will automatically guess what the type is for each file, which you can manually change. You can also remove any files you have accidentally included.

Depending on what type of submission you have made, different files will be mandatory or optional. An example of a complete submission with an mzIdentML result file, along with the related peak list file, and raw data file is shown in the figure below.

Again, for details about the submission types, please see the PRIDE Help submission section

Figure 12 The PX submission tool's ‘Add files’ screen. Here, files that are going to be part of the submission are selected and tagged.

For a full list of all the different file types, see Appendix 1.

Experiment details

Further experimental information is required, either individually for each result file (complete submissions), or overall for the dataset (partial submissions).

In Figure 14, below, an example for a complete submission is shown. In order to reach this screen, the "+ Annotate" button for the result file was clicked (similarly to the previous step for mapping relationships). A partial submssion will go straight to this screen instead, after performing the mapping for relationships.

To enhance your dataset you should add as much available metadata as possible.

Figure 14 PX submission tool, experiment details. Example of a complete submission.

Mandatory information needed for a complete submission: species, tissue, and instrument.

A partial submission also requires modifications to be entered [4].

Ontology terms have to be selected from each of the drop-down menus which have the most commmon options listed. If a required term is not present: select the bottom "Other..." option from the drop-down which will then allow you to search across various ontologies to select a desired term.

Create relationships between files

Raw files need to be mapped to the corresponding result (complete submission) or search engine output files (partial submission). The tool will try to do this automatically depending on the file naming structure, and this can be edited manually using the "+ Relation" button for each result or search output file (Figure 13).

Figure 13 PX submission tool, relationships between files.

Dataset details

Here mandatory details about the dataset are required, such as a title for your submission, experimental and data processing protocol, and experiment type (Figure 11).


Figure 11 PX submission tool, dataset details.

Please note that the description and protocol fields need at least 50 characters to be entered in order to continue.

Final checks and data submission

Once all the relevant information has been added you will have an opportunity to do a final check before you start the submission (Figure 16).

After you click "Submit", your files will be uploaded to PRIDE. This will take some time depending on how large your dataset is, and how fast your internet connection is. When all files have finished transferring to PRIDE, you will receive an e-mail including a submission reference. This is not an accession number to be quoted in manuscripts. It should be used in all communications between you (the submitter) and the PRIDE team. An automated confirmation e-mail will also be sent to your registered e-mail address.

Your submission will then be processed by expert biocurators in the PRIDE team, which may need to contact you in order to improve the quality of the provided metadata. Once everything is corrected (if applicable), your dataset will be loaded into the PRIDE database. After this happens you will recieve another automated e-mail with a unique ProteomeXchange identifier (PXD accession number) and the private reviewer account details. If you had made a complete submission, you will also receive a data DOI.

Figure 16 PX submission tool, submission summary.

In the top-right corner of this screen there is a button called "Export summary file". This will save all the meta-data for your dataset into a summary "submission.px" file. This is useful if making a "bulk" submission through the PX Submission tool, or a direct manual submission to PRIDE via our private Aspera/FTP server. Such manual submissions are useful when dealing with large datasets that cannot be easily managed with the PX Submission tool alone. Full details about this can be found on the PRIDE Help section.

There are a few options possible post-submission, e.g. making the dataset public. These are lsited in our PRIDE Help FAQ.