Large-scale genomics, proteomics and metabolomics technologies have been used to find more precise predictive biomarkers for clinical applications. In this context an urgent need for robust affinity-based sample preparation techniques has emerged that can provide easy-touse and reliable biomarker recovery, identification and detection. Protein phosphorylation analysis using mass spectrometry and applications of enrichment techniques such as IMAC and MOAC in particular is commonly restricted to generic enrichment of phosphorylated residues. Here we demonstrate that molecularly imprinted polymers provide a new dimension in offering the ability to tailor the enrichments towards specific amino acid modifications or peptide sequences. This may reveal hitherto unknown phosphorylation sites or offer a useful tool for targeted phosphoproteomics. We show here that sequence specific binders are capable of specific enrichment of the targeted pTyr peptides directly from in-gel digests of protein from cell lysates. To demonstrate the approach we focused on ZAP-70, a mediating kinase in the TCR signalling cascade with a phosphorylation state being a prognostic factor of Chronic Lymphocytic Leukemia (CLL). The results show that the MIP binders could cleanly enrich phosphopeptides corresponding to the regulatory motif of the ZAP-70 kinase domain.