Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users

Abstract

Core facilities and research infrastructures have become an essential part of the scientific ecosystem. In the field of proteomics, national and international networks and research platforms have been established during the past decade that are supposed to set standards for high-quality services, promote an exchange of professional information, and enable access to cutting-edge, specialized proteomics technologies. Either centralized or distributed, these national and international proteomics infrastructures and technology platforms are generating massive amounts of data for the research community, and support a broad range of translational, computational and multi-omics initiatives and basic research projects.

By delegating part of their work to these services, researchers expect that the core facility adjusts their analytical protocols appropriately for their project to acquire data conforming best research practice of the scientific community. The implementation of quality assessment measures and commonly accepted quality controls in data generation is therefore crucially important for proteomics research infrastructures and the scientists who rely on them.

However, current quality control and quality assessment procedures in proteomics core facilities and research infrastructures are a motley collection of protocols, standards, reference compounds and software tools. Proteomics relies on a customized multi-step workflow typically consisting of sample preparation, data acquisition and data processing, and the implementation of each step differs among facilities. For example, sample preparation involves enzymatic digestion of the proteins, which can be performed in-solution, in-gel, or on-beads, with often different proteolytic enzymes, chemicals, and conditions among laboratories. Data acquisition protocols are often customized to the particular instrument set up, and the acquired spectra and chromatograms are processed by different software tools provided by equipment vendors, third parties or developed in-house.