Submitted: 2018-04-19
Revised: 2025-04-03
Template Rev2016b
1. Administrative Section
Status (New/Update): Update
Group Name: HUPO PSI Quality Control Working Group (PSI-QC WG)
Chair (with affiliation and current email address): Wout Bittremieux (wout.bittremieux@uantwerpen.be) – University of Antwerp, Antwerp, Belgium
Co-Chairs (1 or 2) (with affiliation and current email address): Mathias Walzer (walzer@ebi.ac.uk) – Scientist-at-large
Secretary: None.
Other officers (optional) (with affiliation and current email address):
- Ontology coordinator: Julias Uszkoreit (julian.uszkoreit@rub.de) – Ruhr University Bochum, Bochum, Germany
- Chair emeritus: David L. Tabb (d.l.tabb@rug.nl) – University Medical Center of Groningen, Groningen, the Netherlands
- MaxQuant liaison: Chris Bielow (chris.bielow@fu-berlin.de) – Freie Universität Berlin, Berlin, Germany
Mailing list: psidev-qc-dev@lists.sourceforge.net
2. Description and Objectives
Focus and Purpose
The PSI-QC working group is composed of academic researchers, bioinformatics software developers, and government researchers. The main goal of the PSI-QC working group is to provide a unifying framework for quality control information in biological mass spectrometry, by defining the community-driven standardized mzQC file format and associated controlled vocabulary terms. The PSI-QC working group is a community-driven effort that welcomes any contributions from interested researchers and supporters.
Current projects of the PSI-QC working group are:
- The mzQC file format, a standardized JSON format for the exchange, transmission, and archiving of quality control metrics derived from mass spectrometry.
- Controlled vocabulary development: controlled vocabulary terms related to mass spectrometry quality control are developed in coordination with the PSI-MS/PI working groups.
Goals/Milestones
- ☑️ Publish a peer-reviewed perspective manuscript to announce the PSI-QC working group to the scientific community.
Bittremieux et al. Analytical Chemistry 89, 4474–4479 (2017) doi:10.1021/acs.analchem.6b04310 - ☑️ Analyze and revise the mzQC format for submission to the PSI document process.
- ☑️ Re-evaluate controlled vocabulary terms related to mass spectrometry quality control, and merge these into the PSI-MS controlled vocabulary.
- ☑️ Establish the revised mzQC format and associated controlled vocabulary terms as a HUPO-PSI standard by submitting the format to the PSI Document Process.
- ☑️ Provide and maintain software libraries that can process mzQC files to facilitate its support and adoption in various bioinformatics software tools for handling mass spectrometry quality control data.
Bielow et al. Journal of the American Society for Mass Spectrometry 35, 1875–1882 (2024) doi:10.1021/jasms.4c00174 - ☐ Demonstrate the benefits of mzQC through diverse use cases, geared towards mass spectrometry-based end users across multiple omics applications.
- ☐ Develop analysis and visualization tools tailored for mzQC, to enable intuitive interpretation and reporting of quality control metrics.
- ☐ Supplement prominent mass spectrometry-based biological studies with mzQC quality metrics, to improve transparency and reproducibility.
- ☐ Support the inclusion of mzQC information as part of public data submissions to widely used mass spectrometry data repositories, enhancing data quality tracking and reuse.