Although the PX XML format provides substantial study-level metadata and a list of files submitted with the study, it does not provide for specific sample metadata and a mechanism to link individual files to specific samples of the study. The MAGE-TAB for proteomics format, which is an extension of the original MAGE-TAB format used in transcriptomics, has been recently adapted by ProteomeXchange resources to capture the sample metadata and the experimental design for proteomics experiments. MAGE-TAB for proteomics has two main components: the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF-Proteomics). The MAGE-TAB-Proteomics files are compatible with the original transcriptomics versions, but several adaptations/extensions are included for the proteomics use case. IDF is quite analogous to the PX XML format, although it is less structured and is not as rich in information as PX XML. PX XML files can be easily converted into IDF with some loss of information. SDRF-Proteomics files provide the previously missingand much neededmechanism to provide sample-specific annotations with CV terms, and encode the links from those samples to the submitted data files. Sample attributes are encoded in the columns of the files, where the column definitions are required to be CV terms and the data values are either CV terms or plain scalar values when CV terms are not appropriate. Several ProteomeXchange repositories now accept and process SDRF-Proteomics files upon submission of datasets, and the GitHub repository at provides a mechanism for anyone in the community to manually curate and generate SDRF-Proteomics files for ProteomeXchange datasets that were previously released. The MAGE-TAB for Proteomics effort was primarily driven by the EuBIC-MS group, in collaboration with the PSI. As mentioned above, submission of IDF files is not required since all the information required to create them is made available at submission time.