Evaluation of the Potential Risk of Analyzing Phosphopeptides with Easy-nLC 1200-Coupled Mass Spectrometers

Liquid chromatography–mass spectrometry (LC–MS) is a major tool for the large-scale qualitative and/or quantitative analysis of protein phosphorylation in cells or tissues. The performance of LC is pivotal for the success of phosphoproteomics in both sensitivity and reproducibility. Here, we report that the widely used Easy-nLC 1200 has poor performance in analyzing phosphopeptides, particularly in terms of sensitivity and reproducibility, whereas its predecessor, Easy-nLC 1000, has a much better performance. Therefore, we suggest that Easy-nLC 1200 is not appropriate for LC–MS-based proteomics analysis for samples with a limited amount, particularly phosphopeptides from plants.