The Proteomics Sample Metadata Project aims to standardize the way ProteomeXchange partners and the proteomics community capture the relation between the samples and the data generated within a PX submission. We have adapted the MAGE-TAB v1.1 format to capture necessary metadata for Proteomics experiments to allow automated re-processing. The MAGE-TAB (MicroArray Gene Expression Tabular) is the file format that has been used to store the metadata and sample information on transcriptomics experiments.
By repurposing and extending the MAGE-TAB for Proteomics, we aim to provide a format for future submissions of multiomics experiments to ProteomeXchange partners and better integration with other omics data. The MAGE-TAB is divided in two main files: IDF (Investigation Description Format) and SDRF (Sample and Data Relationship Format). We will describe how these two files are adapted for Proteomics.
The goal is to ensure maximum reusability of the deposited data in proteomics public data repositories. Our work aims to define the minimum information required to report the experimental design of proteomics experiments, enabling the use and reuse of the deposited data by the proteomics community.
IDF
The IDF (Investigation Description Format) file contains fields describing the study, authors/submitters, protocols, publications (Read Section). ProteomerXchange resources developed a file format called submission.px which captures the same information as the MAGE-TAB IDF. We have developed a set of tools to automatically translate from submission.px to IDF.
SDRF (SDRF-Proteomics)
While the experiment general description is captured for all the PX submissions and experiments, the Sample to Data information is missing (or not standardized) for all PX datasets. The standardization of the SDRF (within MAGE-TAB) for proteomics is the main objective of this project (Read more about SDRF-Proteomics).
Current Specification Document
The current version of the specification document (going through the PSI public review process is available here).
More information is available here.