Selective enrichment techniques are essential for mapping of protein posttranslational modifications (PTMs). Phosphorylation is one of the PTMs which continues to be associated with significant analytical challenges. Particularly problematic are tyrosine-phosphorylated peptides (pY-peptides) resulting from tryptic digestion which commonly escape current chemo- or immuno- affinity enrichments and hence remain undetected. We here report on significant improvements in this regard using pY selective molecularly imprinted polymers (pY-MIPs). The pY-MIP was compared with titanium dioxide (TiO2) affinity based enrichment and immunoprecipitation (IP) with respect to selective enrichment from a mixture of 13 standard peptides at different sample loads. At a low sample load (1 pmol of each peptide), IP resulted in enrichment of only a triply phosphorylated peptide whereas TiO2 enriched phosphopeptides irrespective of the amino acid side chain. However, with increased sample complexity, TiO2 failed to enrich the doubly phosphorylated peptides. This contrasted with the pY-MIP showing enrichment of all four tyrosine phosphorylated peptides at 1 pmol sample load of each peptide with a few other peptides binding unselectively. At an increased sample complexity consisting of the standard peptides spiked into mouse brain digest, the MIP showed clear enrichment of all four pYpeptides.

Protein phosphorylation at distinct tyrosine residues (pY) is essential for fast, specific, and accurate signal transduction in cells. Enrichment of pY-containing peptides derived from phosphoproteins is commonly facilitated by use of immobilized anti-pY antibodies prior to phosphoproteomics analysis by mass spectrometry. We here report on an alternative approach for pY-peptide enrichment using inexpensive pY-imprinted polymer (pY-MIP). We assessed by mass spectrometry the performance of pY-MIP for enrichment and sequencing of phosphopeptides obtained by tryptic digestion of protein extracts from HeLa cells. The combination of pY-MIP- and TiO2-based phosphopeptide enrichment provided more than 90% selectivity for phosphopeptides. Mass spectrometry signal intensities were enhanced for most pY-phosphopeptides (approximately 70%) when using the pY-MIP-TiO2 combination as compared to TiO2 alone. pY constituted up to 8% of the pY-MIP-TiO2-enriched phosphopeptide fractions. The pY-MIP-TiO2 and the TiO2 protocols yielded comparable numbers of distinct phosphopeptides, 1693 and 1842, respectively, from microgram levels of peptide samples. Detailed analysis of physicochemical properties of pY-MIP-TiO2-enriched phosphopeptides demonstrated that this protocol retrieved phosphopeptides that tend to be smaller (<24 residues), less acidic, and almost exclusively monophosphorylated, as compared to TiO2 alone. These unique properties render the pY-MIP-based phosphopeptide enrichment technique an attractive alternative for applications in phosphoproteomics research.

Two templating approaches to produce imprinted phosphotyrosine capture beads with a controllable pore structure are reported and compared with respect to their ability to enrich phosphopeptides from a tryptic peptide mixture. The beads were prepared by the polymerization of urea-based host monomers and crosslinkers inside the pores of macroporous silica beads with both free and immobilized template. In the final step the silica was removed by fluoride etching resulting in mesoporous polymer replicas with narrow pore size distributions, pore diameters approximate to 10 nm and surface area > 260 m(2) g(-1). The beads displayed pronounced phosphotyrosine affinity and selectivity in binding tests using model peptides in acetonitrile rich solutions with a performance surpassing solution polymerized bulk imprinted materials. Tests of the beads for the enrichment of phosphopeptides from tryptic digests of twelve proteins revealed both pY/pS and pY/Y selectivity. This was reflected in a nearly 6-fold increase in the enrichment factor of a 23-mer pY-peptide and pY/pS normalized intensity ratios up to 1.5, when comparing the template mesoporous beads with the bulk materials.

We report on the design and characterization of imprinted cationic host polymers for selective trapping of phosphoserine and phosphotyrosine peptides. A series of imidazolium host monomers were synthesized and characterized with respect to binding affinity and stoichiometry of interaction with salts of phenylphosphonic acid. The strongest binders were subsequently used for the preparation of imprinted polymers in the form of crushed monoliths, using Fmoc-phosphotyrosine-ethyl ester or Fmoc-phosphoserine-ethyl ester as templates in combination with a hydrophilic crosslinking monomer. The polymers were compared with respect to binding and its dependence on solvent, and whether charged or uncharged host monomers were used. The recipes were subsequently implemented in the capillary monolith format for evaluation by micro-liquid chromatography in both buffered and organic media. Results from both tested formats reveal that the cationic host polymers displayed enhanced recognition in polar and buffered media, in contrast to neutral urea-based hosts which showed best results in acetonitrile rich mobile phases.