Managing and reusing public proteomics & metabolomics data
The Proteomics and Metabolomics Team, led by Juan Antonio Vizcaíno, develops an ecosystem of resources, tools, formats, and workflows for the representation, deposition, analysis, and reuse of public proteomics and metabolomics data. The team is responsible for the PRIDE and MetaboLights databases, for proteomics and metabolomics data.
The team follows an open-source, open-data approach and is a major contributor to community standards, in particular the Proteomics Standards Initiative (PSI) of the international Human Proteome Organization (HUPO), and ProteomeXchange Consortium.
The MetaboLights database is a data repository for all types of metabolomics data, including mass spectrometry and NMR.
The PRoteomics IDEntifications (PRIDE) database at the European Bioinformatics Institute (EMBL-EBI, Hinxton, Cambridge, UK) enables public data deposition of mass spectrometry (MS)-based proteomics data, providing access to the experimental data described in scientific publications.
PRIDE stores datasets coming from all proteomics experimental approaches, with a focus on discovery-driven techniques such data-dependent acquisition (DDA) and data-independent acquisition (DIA) bottom-up proteomics, but also top-down proteomics and MS imaging, among others. The PRIDE team has led within the Proteomics Standards Initiative (PSI) organization, the creation and implementation of multiple standard open file formats such as mzTab, mzIdentML and mzML to store, process and visualize the proteomics data deposited.
PRIDE resources and tools ecosystem, including the two main resources: PRIDE Archive and PRIDE Peptidome.
The PRIDE database is one of the founding members of the ProteomeXchange Consortium (PX) in 2011. PX defines the guidelines for data submission and dissemination of public proteomics data worldwide. Additionally, in 2017, PRIDE became an ELIXIR core data resource and ELIXIR deposition database, recognizing its key role in the life sciences.
PRIDE resources have two main missions for the proteomics community: (i) support data deposition and quality assessment of submitted proteomics experiments, to help reproducible research; and (ii) promote and facilitate the reuse of public proteomics data, and disseminate high-quality proteomics evidences using PRIDE Peptidome into added-value resources, including among others Ensembl, UniProt and Expression Atlas.
The MetaboLights database at the European Bioinformatics Institute (EMBL-EBI, Hinxton, Cambridge, UK) enables public data deposition of different types of metabolomics data (e.g. MS and NMR), providing access to the experimental data described in scientific publications. The team is also a major contributor to community data standards in metabolomics such as mzTab-M.
