How to submit MS proteomics data to ProteomeXchange via the PRIDE database.

Area of Science:

• Proteomics
• Bioinformatics
• Data Science

Background:

• The ProteomeXchange (PX) consortium aims to standardize MS-based proteomics data submission and dissemination.
• The PRIDE database serves as the primary submission portal for MS/MS datasets within the consortium.

Purpose of the Study:

• To provide a step-by-step guide for submitting MS/MS datasets to ProteomeXchange via the PRIDE database.
• To detail the 'complete' and 'partial' submission workflows and available tools.

Main Methods:

• Explanation of the submission process for MS/MS data sets to ProteomeXchange.
• Description of two distinct submission workflows: 'complete' and 'partial'.
• Illustrative example using a dataset with identification and quantification data (PXD000764).

Main Results:

• A clear, step-by-step protocol for data submission is presented.
• The manuscript outlines the differences and use cases for complete and partial submissions.
• An example dataset (PXD000764) demonstrates the described submission process.

Conclusions:

• Standardized submission of proteomics data to ProteomeXchange via PRIDE is facilitated by this guide.
• The described workflows and tools streamline the process for researchers.
• Effective data sharing is crucial for advancing MS-based proteomics research.