The reproducibility of liquid chromatography separation technology and its potential impact on large scale plant metabolomics experiments

• Improved phenylpropanoid profiling for plant phytochemical studies.
• Comparison of separation modules for technical performance.
• Impact of UHPLC performance on large-scale metabolomic studies.

Unraveling the constituents of biological samples using HPLC is a central core technology in metabolomics experiments. Consistency in retention time across many samples is a critical criterion for judging the quality of a data set, which must be met before further analysis are possible. Here, the performance of two ultra high-performance liquid chromatography (UHPLC) systems has been compared using an established separation protocol optimized for phenylpropanoids, a class of secondary compounds found in plants displaying intermediate polarity. The two systems differed markedly with respect to their reproducibility and pressure stability. The standard deviation of the retention time of representative peaks differs up to 30-folds between the systems. Adjustments made to the gradient profiles succeeded in equalizing their level of performance. However, the modifications made to the separation protocol reduced the quality of the separation, particularly of the more rapidly eluting components, and lengthened the run time.