The© highly© selective© capture© of© phosphopeptides© from© proteolytic© digests© is© a© great© challenge for© the© identification© of© phosphoproteins© by© mass© spectrometry.© In© this© work,© the© zirconium phosphonate-modified© magnetic© Fe 3 O 4 /SiO 2© core/shell© nanoparticles© have© been© synthesized and© successfully© applied© for© the© selective© capture© of© phosphopeptides© from© complex© tryptic digests© of© proteins© before© the© analysis© of© MALDI-TOF© mass© spectrometry© with© the© desired convenience©of©sample©handling.©The©ratio©of©magnetic©nanoparticle©to©protein©and©the incubation© time© for© capturing© phosphopeptides© from© complex© proteolytic© digests© were© investigated,© and© the© optimized© nanoparticle-to-protein© ratio© and© incubation© time© were© between© 15:1© to 30:1© and© 30© min,© respectively.© The© excellent© detection© limit© of© 0.5© fmol© -casein© has© been© achieved by© MALDI-TOF© mass© spectrometry© with© the© specific© capture© of© zirconium© phosphonate-modified magnetic©Fe 3 O 4 nanoparticles.©The©great©specificity©of©zirconium©phosphonate-modified magnetic© Fe 3 O 4© nanoparticles© to© phosphopeptides© was© demonstrated© by© the© selective© capture of© phosphopeptides© from© a© complex© tryptic© digest© of© the© mixture© of© ␣-casein© and© bovine© serum albumin© at© molar© ratio© of© 1© to© 100© in© MALDI-TOF-MS© analysis.© An© application© of© the© magnetic nanoparticles© to© selective© capture© phosphopeptides© from© a© tryptic© digest© of© mouse© liver© lysate was© further© carried© out© by© combining© with© nano-LC-MS/MS© and© MS/MS/MS© analyses,© and .©The©comprehensive©understanding©of©biological processes© requires© the© characterization© of© protein© phosphorylation© at© molecular© level.© Mass© spectrometry© is© a fundamental© tool© for© detecting© and© mapping© the© phosphoryl© modifications© of© proteins© [2][3][4][5].© However,© due© to the© minimal© amount© of© phosphorylation© found© on© proteins©and©the©serious©ion©suppression©phenomenon resulting© from© the© proteolytic© complexity© [6],© selective capture© of© phosphopeptides© from© complex© proteolytic products© has© been© remaining© quite© a© challenge© in© the field© of© proteomics.Up© to© now,© a© variety© of© approaches© have© been© developed© for© selective© determination© of© phosphopeptides© and thus© improve© the© detection© sensitivity© of© mass© spectrometry,© such© as© chemical© derivatization© [7][8][9],© immunoprecipitation© [10,© 11],© strong© ion-exchange© [12,© 13],© and© metal affinity© technique© [14© -24].© Among© these,© the© metal© affinity technique© using© immobilized© metal© ions© or© metal© oxides as© the© affinity© moieties© to© phosphopeptides© was© the© most frequently© applied© method,© and© has© been© widely© applied for©the©selective©capture©or©even©purification©of©phos-phopeptides© via© the© specific© binding© between© the© metal moieties©and©the©phosphoryl©groups©of©peptides©and proteins.© For© instance,© the© immobilized© metal© ions© of© Fe 3ϩ , Ga 3ϩ ,© and© Zr ...