Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 3: De Novo Peptide Sequencing Using Electrospray Tandem Mass Spectrometry

Abstract

Tandem mass spectrometry (MS–MS) is an important technique routinely used to provide structural information about analytes of interest. One major application of tandem mass spectrometry is in the field of proteomics, which routinely uses MS–MS experiments to help identify peptides and proteins. In this experiment, students learn how to perform a tandem mass spectrometry experiment on a selected peptide ion using an ion-trap mass spectrometer and how to use the resulting data to sequence the peptide de novo. While the majority of protein and peptide identification done using mass spectrometry relies on database search algorithms, it is still important for a trained scientist to compare the computer results with the empirical data to make a judgment as to how well the two correlate. It is therefore important that students be exposed to peptide sequencing and learn how this can be done without a database to prepare them for research in the proteomics field. We have included several representative peptide fra...