# What Have Data Standards Ever Done for Us?

## TL;DR

This paper reviews how data standards developed by the Human Proteome Organization Proteomics Standards Initiative have improved data sharing and analysis in proteomics.

## Contribution

The paper highlights the impact of community-driven data standards on enabling loss-free data transfer and reanalysis in proteomics.

## Key findings

- Standards allow seamless data transfer between instruments, software, and databases.
- Data repository consortia can merge diverse datasets using standardized formats.
- Improved dataset annotation is needed to enhance reanalysis success.

## Abstract

The Human Proteome Organization Proteomics Standards Initiative has been successfully developing guidelines, data formats, and controlled vocabularies for both the field of molecular interaction and that of mass spectrometry for more than 20 years. This review explores some of the ways that the proteomics community has benefitted from the development of community standards and takes a look at some of the tools and resources that have been improved or developed as a result of the work of the Human Proteome Organization-Proteomics Standards Initiative.

•The Human Proteome Organization Proteomics Standards Initiative publishes data standards for experimental protein science.•Standards allow loss-free data transfer between instruments, software, and databases.•Data repository Consortia merge diverse datasets using standard data formats.•Data generators need to improve dataset annotation to support successful reanalysis.

The Human Proteome Organization Proteomics Standards Initiative publishes data standards for experimental protein science.

Standards allow loss-free data transfer between instruments, software, and databases.

Data repository Consortia merge diverse datasets using standard data formats.

Data generators need to improve dataset annotation to support successful reanalysis.

The HUPO-Proteomics Standards Initiative (PSI) publishes guidelines, data formats, and controlled vocabularies describing molecular interactions and mass spectrometry experiments. These standards have enabled the transfer of information between data generation, analysis, and repositories. Users have benefitted from an ever-increasing volume of consistently formatted and annotated information available for reanalysis. One route this has been made available to users is via knowledge bases such as UniProt which imports information on protein interactions, posttranslation modifications, and protein translation evidence from large-scale data Consortia.