Open-Source System Suitability: Mass Spectrometry Query Language Lab (MassQLab)

Rationale

Reproducible analytical instrumentation system performance is critical for mass spectrometry, particularly metabolomics, aptly named system suitability testing. We identified a need based on literature reports that stated only 2% of papers performed system suitability testing.

Methods

We report MassQLab, built upon open-source, vendor-agnostic software called the mass spectrometry query language (MassQL). MassQL, implemented in MassQLab, provides freedom for researchers to choose their analyte/s, mass spectrometry system (including liquid chromatography—mass spectrometry), and metrics of performance.

Results

In this report, we describe the use of MassQLab, demonstrate the construction of the required MassQL query, common metrics of performance (i.e., extracted ion chromatograms), uncommon metrics (i.e., MS/MS product ion spectra), and discuss insights gained about performance—including issues requiring correction prior to sample analysis.

Conclusions

MassQLab is a flexible solution for system suitability testing for mass spectrometry-based analytical measurements. Deficits in analytical performance, while unavoidable and rare, were noted prior to data collection and corrected. The open-source and adaptable nature of MassQLab will empower researchers and lead to improved implementation of system suitability testing.