Published April 18, 2017 | Version v1
Journal article Open

The Human Proteome Organization–Proteomics Standards Initiative Quality Control Working Group: Making quality control more accessible for biological mass spectrometry

  • 1. Department of Mathematics and Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerp, Belgium
  • 2. Department of Computer Science, University of Tübingen, Tübingen 72076, Germany
  • 3. Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz D 55131, Germany
  • 4. National Center for Protein Science, No. 38, Science Park Road, Changping District, Beijing 102206, China
  • 5. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
  • 6. Medical Bioinformatics, Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum 44801, Germany
  • 7. Division of Molecular Biology and Human Genetics, Stellenbosch University Faculty of Medicine and Health Sciences, Tygerberg Hospital, Francie Van Zijl Drive, Cape Town 7505, South Africa


To have confidence in results acquired during biological mass spectrometry experiments, a systematic approach to quality control is of vital importance. Nonetheless, until now, only scattered initiatives have been undertaken to this end, and these individual efforts have often not been complementary. To address this issue, the Human Proteome Organization–Proteomics Standards Initiative has established a new working group on quality control at its meeting in the spring of 2016. The goal of this working group is to provide a unifying framework for quality control data. The initial focus will be on providing a community-driven standardized file format for quality control. For this purpose, the previously proposed qcML format will be adapted to support a variety of use cases for both proteomics and metabolomics applications, and it will be established as an official PSI format. An important consideration is to avoid enforcing restrictive requirements on quality control but instead provide the basic technical necessities required to support extensive quality control for any type of mass spectrometry-based workflow. We want to emphasize that this is an open community effort, and we seek participation from all scientists with an interest in this field.

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see


2017_Bittremieux_The Human Proteome Organization–Proteomics Standards Initiative Quality Control Working Group.pdf