Integrated Single-Tip IMAC-HILIC Enables Simultaneous Analysis of Plant Phosphoproteomics and N-Glycoproteomics

Protein phosphorylation and N-glycosylation are key post-translational modifications (PTMs) in plants that regulate critical signaling processes. However, coanalysis of these PTMs is often complicated by their relatively low abundance and divergent enrichment requirements. Here, we present a single-tip IMAC-HILIC approach that integrates immobilized metal affinity chromatography (IMAC) and hydrophilic interaction chromatography (HILIC) materials within one pipet tip, enabling concurrent enrichment and sequential elution of phosphopeptides and N-glycopeptides. This integrated workflow effectively reduces phosphopeptide coelution during N-glycopeptide elution and streamlines sample processing. In direct comparison with the tandem-tip TIMAHAC method, our single-tip strategy achieves a comparable identification depth and offers superior quantitative accuracy for N-glycopeptides. We further demonstrate its applicability by examining the impact of calcium deprivation in Arabidopsis, revealing distinct global changes in both the phosphoproteome and N-glycoproteome. Our optimized protocol thus provides a straightforward and high-throughput platform for dual PTM profiling in complex plant samples, paving the way for broader investigations of PTM crosstalk in diverse physiological and stress responses.