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.