In mass spectrometry based lipidomics, inconsistent analytical methods may lead to irreproducible and biased lipid quantification. Community efforts have already been undertaken to harmonize both sample preparation and data analyses [1], while currently there is no rapid and robust test if a mass spectrometer was correctly set up for lipidomics analysis.
We developed rapid, technically straightforward and automated quality control protocol for shotgun lipidomics. Ten anonymized laboratories participated in five months trial by performing shotgun analysis of a mix of lipid standards under routine settings. Seven key parameters - mass accuracy, mass resolution, validity of isotopic distribution, lipid class response, ion source fragmentation, sensitivity and fragmentation efficiency – were monitored. It allowed us to evaluate the impact of instrument settings, calibration, analyte composition and frequent contaminants.
The QC test only takes 5-minutes and the results are assesses by web accessible “QC Shotgun” software (Fig.1) which helps to document longitudinal performance and stability of high-resolution mass spectrometers tuned for shotgun lipidomics.
Fig.1 Commercial Ultimate SplashMix is diluted, plated and FT MS and FT MS/MS spectra are acquired for approx. 3 minutes. Peak lists are exported and analyzed by QC Shotgun web application that computes seven cumulative indices critical for shotgun lipidomics analyses, saved and compared with previous measurements.
References
1. Lipidomics Standards Initiative Consortium. Lipidomics needs more standardization. Nat Metab 1, 745–747 (2019). https://doi.org/10.1038/s42255-019-0094-z
