Proteomics repositories, PRIDE database and re-use of public proteomics data

Trainers: Juan A. Vizcaino, David García-Seisdedos, Deepti J Kundu, Ananth Prakash, Shengbo Wang

Overview: In this session, you will find an overview of open data standard and proteomics data repositories, highlighting those that are part of the ProteomeXchange Consortium. Next, he will explain how to submit and access data in EMBL-EBI’S PRIDE database, the most used ProteomeXchange database. Finally, he will talk about data reuse of public proteomics data.

Afterwards, you will be introduced to the PRIDE tools you can use to submit data to or access data in the PRIDE database.

Learning outcomes

By the end of this session you will be able to:

  • Identify the main open data standards in the field of proteomics, and which of them are adopted the most.
  • Explain why you should share your proteomics data.
  • Cite the different data types stored in MS proteomics repositories.
  • Find the main existing resources for proteomics data (highlighting those that are part of ProteomeXchange) and their main characteristics
  • Describe how to submit data to the PRIDE database, including the use of the PX submission tool
  • Describe how to access data in the PRIDE database, including the web interface
  • Describe how to create well-annotated data submissions
  • Cite the main types of data reuse of public proteomics data, and learn about some concrete published examples.

Materials:

2021 lecture recording:

2021 lecture recording:

2021 lecture recording:

Practical session overview: In this session, you will learn about PRIDE tools that you can use to submit data to or access data on PRIDE database.

Practical materials:

Previous editions materials