Identifying gel-separated proteins using in-gel digestion, mass spectrometry, and database searching: Consider the chemistry.

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is an important bioanalytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. This is an especially powerful tool when combined with gel separation of proteins and database mining using the mass spectral data. Currently, few hands-on laboratory opportunities exist for undergraduate students to master this technique despite the usefulness of this technique in biological research. One reason for this lack of incorporation into the teaching curriculum is the relatively low number of published laboratory experiments that demonstrate how mass spectrometry can be incorporated into undergraduate laboratories. We present a simple experiment designed to introduce students to the analysis of gel separated proteins using mass spectrometry. In this experiment, students analyze one or more proteins using gel electrophoresis, followed by in-gel digestion, MALDI-time-of-flight (TOF) mass spectrometry and database mining. The experiment also demonstrates how erroneous results can be obtained if careful attention is not paid to all aspects of the experimental process. The data presented here can be used in a classroom or laboratory setting even if hands-on access to a MALDI-TOF mass spectrometer is not possible.