Incremental Modification in the Existing Approaches for Affinity Chromatographic Enrichment of Phosphoproteins Improves Their Profile in Liquid Chromatography-Tandem Mass Spectrometry Analysis

Abstract

Cell signalling is a vital process in cell physiology, which is driven by protein phosphorylation. Global phosphoproteome analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) has thus gained importance in cell signalling research. However, phosphoprotein identification by LC-MS/MS in whole cell lysates, which are complex protein mixtures, is hindered by their poor ionization coupled with suppression of peaks due to low abundance. Enrichment by immobilized metal ion- and metal oxide-affinity chromatography (IMAC and MOAC), which preferentially enrich multi- and mono-phosphorylated proteins, respectively, have improved their detection by MS. However, preferential enrichment limits phosphoproteome coverage in global analyses of cell lysates which contain mono- and multi-phosphorylated proteins. Improvement in their coverage by sequential elution approach that exploits the complementary chemistries of these matrices has been reported. In this study, we observed that the number of phosphoproteins detected using the sequential elution approach was lower (∼250-400) as compared to the theoretically predicted number (>500) based on their reported 30% abundance in the cell proteome (1700-2200 proteins detected by MS in our cell lines). Acknowledging the merit of using multiple matrices, we used IMAC and MOAC individually and pooled the data. We observed a remarkable increase (>30%) in phosphoproteome coverage. Further, though 98% of phosphoproteins were enriched by IMAC, among the remaining 2%, those detected exclusively by MOAC were biologically important. This justified the use of multiple matrices. Thus, an incremental modification of using multiple matrices individually rather than sequentially and pooling the data markedly improved the phosphoproteome coverage, which can positively impact cell signalling research.

Keywords: affinity chromatography; enrichment; phosphoproteins.

FIGURE 1

Number of phosphoproteins enriched by different methods. The number of phosphoproteins identified by each enrichment method represents a total of identities obtained from biological duplicates, each run in triplicate for MS analysis for K562/S and K562/R.

FIGURE 2

Evaluation of phosphoprotein enrichment methods. The number of phosphoproteins identified following: (A, B) sequential enrichment through the two affinity chromatography materials (methods 3 and 4) and (C, D) independent elution through the two matrices (methods 1 and 2) for K562/S and K562/R cells. FT: flow‐through.