In about 90 % of cancer cases, the development of the disease is caused by the accumulation of mutations occurring in somatic cells. The goal of this study is to exploit existing data sets from the NCI-60 human cancer cell line panel with the help of bioinformatic tools in order to identify genomic sequence variants in proteomic tandem mass spectrometry data, with a particular focus on the identification of somatic variants. The search of 2,552,251 retrieved tandem mass spectra against 45,233 variants obtained after several processing steps yielded to the successful identification of a total of 762 variants in 355 unique proteins across the 9 NCI-60 cell lines under investigation, including 728 germline variants and 34 somatic variants. Certain germline variants were nonetheless present in several cell lines at the same time, thus constituting a final total of 406 unique variants identified.