Microalgae-derived quality control material for reproducible and scalable LC-MS system suitability testing

Ensuring the accuracy and reliability of liquid chromatography-mass spectrometry (LC-MS/MS)-based proteomic analysis requires robust quality control (QC) strategies. However, widely used cell line-based QC materials present challenges in reproducibility, scalability, and ethical compliance. In this study, we developed a microalgae-derived QC material based on Synechocystis sp. PCC6803 and evaluated its suitability for LC-MS/MS system performance monitoring. The Synechocystis-based QC samples demonstrated high identification reproducibility, with 76% of the protein groups being consistently detected across five replicates and maintaining a median coefficient of variation (CV) of 6.7% in quantitative precision. Furthermore, QC peptides exhibited excellent linearity (R² ≥ 0.98) and reproducibility (CV ≤ 12.06%) across varying injection amounts. These results indicate that Synechocystis-derived QC materials provide a reproducible and scalable approach that complements conventional QC workflows. They are particularly well suited for routine LC-MS/MS system performance monitoring in proteomics workflows involving non-human or mixed biological samples.