As a new, fast and easy-preformed method, nanodiamond has been used to study noncovalent interaction by MALDI-MS. The diamonds covered with "bait analyte" were added into the solution of "fish analyte", and then separated with nanodiamonds by centrifugation and washed by water for final MALDI-MS analysis. At the same time, mass spectrum of supernatant can also provide useful information by comparison with that of original solution without treatment by diamonds. This platform can be used to study inter-molecular noncovalent interaction and can further find its application to selectively enhanced MALDI-MS analysis, as the example of PL-coated nanodiamonds used in mass analysis of phosphopeptides.