MS/MS experiments generate hundreds to tens of thousands of fragment ion spectra during the experiment. In the peptide identification, MS/MS spectra are often identified by database searching algorithms such as SEQUEST and Mascot. Most database searching algorithms calculate score functions to compare the experimental MS/MS spectra with theoretical MS/MS spectra of certain peptides derived from protein sequence databases. However, these indirect methods are vulnerable to potential errors. Thus, some spectra may not be assigned to peptides. To overcome these limitations, we propose a novel algorithm called Finding Identical Spectra for Homogenous peptide (FISH) by using two-stage clustering algorithm. Our proposed FISH algorithm can cluster spectra from the same peptide as a group based on the direct comparison. That is, through all possible pair-wise comparisons, our FISH method provides a set of spectra from the same peptide. To investigate the efficiency of our proposed method, we performed Nano-LC-MS/MS experiment for human tissue samples. Also, we conducted the simulation study to compare the performance of our proposed method with other database searching methods. Our simulation study showed that FISH yielded higher sensitivity than the other methods.