Quality control

Communicating MS quality information in mzQC with Python, R and Java

Bielow C, Hoffmann N, Jimenez-Morales D, Van Den Bossche T, Vizcaíno JA, Tabb DL, Bittremieux W, Walzer M

J. Am. Soc. Mass Spectrometry · 2024 doi: 10.1021/jasms.4c00174 ↗ github.com/MS-Quality-Hub ↗

The idea

A data standard is only as useful as the software that supports it. This work delivers reference libraries for mzQC in Python, R and Java, so quality-control metrics for mass-spectrometry runs can be written, exchanged and validated consistently across the tools a lab already uses.

Key concepts

mzQC is a lightweight JSON format from the HUPO-PSI Quality Control working group.

Metrics are grouped in runQuality / setQuality elements with provenance metadata.

Each metric is anchored to a PSI-MS controlled-vocabulary term for unambiguous meaning.

What we found

Parallel, interoperable implementations in Python, R and Java with consistent behaviour.

Reading, writing and validation against the official mzQC specification.

Released as open source under the MS-Quality-Hub organisation to drive adoption.