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A proteomics sample metadata representation for multiomics integration and big data analysis

The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis.

Here we introduce an extension and implementation of the MAGE-TAB format for proteomics (MAGE-TAB-Proteomics). The format has been developed in collaboration with the Proteomics Standards Initiative (PSI), the organization in charge of developing open-standard formats in the field. We have also developed general guidelines about what information needs to be encoded in MAGE-TAB to improve the reproducibility and enable the reanalysis of proteomics datasets. In addition, we have crowdsourced the annotation of over 200 existing public datasets according to these guidelines, covering different analytical methods and experimental designs. Finally, we have developed an ecosystem of tools to validate MAGE-TAB-Proteomics files and integrate the metadata in the PRIDE database, the most popular PX resource. The full specification document describing all aspects of MAGE-TAB-Proteomics version 1.0, the current implementations, as well as application examples, is available at the PSI website.

Read more in our Nature Communications paper!