In our current work, we describe how open tubular-immobilized metal-ion affinity chromatography (OT-IMAC) capillary columns connected to a solid phase microextraction (in-tube SPME) device can be used for the enrichment of phosphopeptides. A phosphonate modified silica nanoparticle (NP)-deposited capillary was prepared by liquid phase deposition (LPD), and used for the immobilization of Fe(3+), Zr(4+) or Ti(4+). The enrichment capacities of three different OT-IMAC capillary columns were compared by using tryptically digested alpha-casein as sample. The improved extraction efficiency in our technique was demonstrated by comparing to a directly modified capillary, and a comparison of phosphopeptide extraction from simple and complex samples was tested for both modes. Our results show that the NP-IMAC-Zr(4+) capillary column can be used to selectively isolate phosphopeptides from real samples, and can enrich for beta-casein phosphopeptides from concentrations as low as 1.7x10(-9) M.