A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities

Quality control procedures play a pivotal role in ensuring
the
reliability and consistency of data generated in mass spectrometry-based
proteomics laboratories. However, the lack of standardized quality
control practices across laboratories poses challenges for data comparability
and reproducibility. In response, we conducted a harmonization study
within proteomics laboratories of the Core for Life alliance with
the aim of establishing a common quality control framework, which
facilitates comprehensive quality assessment and identification of
potential sources of performance drift. Through collaborative efforts,
we developed a consensus quality control standard for longitudinal
assessment and adopted common processing software. We generated a
4-year longitudinal data set from multiple instruments and laboratories,
which enabled us to assess intra- and interlaboratory variability,
to identify causes of performance drift, and to establish community
reference values for several quality control parameters. Our study
enhances data comparability and reliability and fosters a culture
of collaboration and continuous improvement within the proteomics
community to ensure the integrity of proteomics data.