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

Document Type

Article

Publication Date

10-6-2021

Publication Title

Nat Commun

Keywords

washington; seattle; isb; Genomics; Big Data; Data Analysis; Databases, Protein; Humans; Metadata; Proteomics; Reproducibility of Results; Software; Transcriptome

Abstract

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 propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.

Department

Institute for Systems Biology

Share

COinS