- Tandem-MS is a mass spectrometry based technique for identifying proteins in a biological sample. The proteins are first digested into shorter peptides using a protease such as Trypsin before mass spectrometric analysis. Tandem MS referes to the method of scanning inside the mass spectrometer (MS). A first MS scan is used visualise the peptide ions are selected inside the MS. Ions of interest are selected and fragmented, usually via collision with neutral gas molecules. A second MS scan (hence 'Tandem') acquires data on the fragment spectrum. The fragment spectra can be identified by manual peak assignment, or in a high-throughput manner by searching against theoretical spectra generated from a database of known protein sequences, such as UniProtKB.