In recent years, an open search of tandem mass spectra has greatly promoted the detection of post-translational modifications (PTMs) in shotgun proteomics. However, post-processing of the results from open searches remains an unsatisfactorily resolved problem, which hinders the open search mode from wide practical use. PTMiner is a software tool based on dedicated statistical algorithms for reliable filtering, localization and annotation of the modifications (mass shifts) detected by open search. Furthermore, PTMiner also supports quality control and re-localization of modifications identified by the traditional closed search. In this protocol, we describe how to use PTMiner for the two search modes. Currently, the search engines supported by PTMiner include pFind, MSFragger, MaxQuant, Comet, MS-GF + and SEQUEST.