Image credit: PRIDE

The PRIDE submission tool is the default submission method for contributing your data to the PRIDE Archive. The tool is a open-source stand-alone wizard that can be downloaded from the PRIDE website. Once you have downloaded the tool, it will walk you through a set of simple steps for uploading your data, as well as annotating, linking, and transferring the files required in a given dataset.

Steps for submission: 

1. Log in with your PRIDE account email and password
2. Provide details about your submission, such as the title, a list of keywords (in a comma separated format), a brief description of the dataset (PRIDE recommends this be similar to the abstract of your corresponding publications), and a sample processing/data processing protocol. You will also have to select the mass spectrometry experiment type you used from a dropdown menu. 
3. Upload your files by clicking the "add files" button in the top left corner. Make sure you are following best practices for file naming, such as providing descriptive names that indicate the contents of each file, and removing special characters from all files names. Use underscores rather than spaces when separating words. 
   • Depending on the files provided and the type of submission, the tool will try to link the relation between files and also the file type. Check the submission details page for more information on making submissions that contain mzIdentML or mzTab files. 
4. Calculate the checksums of your files when prompted. The tool will provide the calculation for you. If a file is very large, you can skip the checksum calculation by pressing "No" and then "Next" at this stage. 
5. Provide additional metadata for each Result file. For mzTab files, this metadata will usually import automatically. For mzIdentML, you will have to enter it manually. In both cases, the Species, Tissue, and Instrument Information are necessary. Check the submission details page for more information on the required additional metadata.
6. Provide contact details for your lab head. 
7. Provide optional metadata annotation. It is recommended you complete this step if your data is being republished, already has a PubMed ID associated with it, is part of a larger umbrella project, or is associated with data published in other repositories. 
8. Review your files and submission information. 
9. Initiate the upload process to PRIDE. Once the upload is finished, an e-mail will be sent to you to confirm that all your files have been uploaded successfully and that they are waiting to be validated. If for any reason the tool crashes at this point, the Submission Tool can be restarted and the file upload will attempt to restart in the same point before it did.

Requesting a Globus Shared Folder

• Log onto the PRIDE site 
• Under your profile, click the New Submission tab
• Follow the onscreen instructions 

Uploading files

• Install and configure Globus connect personal
• If you encounter any issues in the above step, refer to Troubleshooting Guide
• Go through this Globus tutorial
• Login to the Globus web
• Navigate to FILE MANAGER
• Click on one of the Collection text box to select your collection (This is the one you created using Globus connect personal)
  • You can find it under Your Collections tab.
  • Make sure Globus connect personal application is running on your machine
• Click on the other Collection text box to select PRIDE Submissions collection.
  • You can either search for it or you can find it under Shared With You tab.
• Choose the appropriate folder from the PRIDE Submissions collection and upload all the files including checksum.txt and submission.px

You can troubleshoot issues with Globus using the troubleshooting guide.

PRIDE has also uploaded the following video to guide you through the GLOBUS submission process: 

• How to manually upload a proteomics dataset to PRIDE Archive database