With the advance of mass spectrometry and experimental techniques, a huge amount of mass spectrometry (MS) data has been accumulated rapidly in the past few years. Usually, different database search engines are used to analyze the MS data for peptide and protein identification. Meanwhile, selection of all those assignments that are actually correct is one of the most daunting tasks in mass spectrometry based proteomics investigations. Target-decoy searching strategy has become one of the most popular strategies to control the fasle identification in MS/MS data analysis. In this paper, we first introduce the workflow of target-decoy database searching strategy. Then we summarize the quality control tools based on the target-decoy searching strategy. Besides, we point out the deficiency of target-decoy searching strategy and put forward mending measures. Finally, we carry on summary and outlook to target-decoy searching strategy.