Introduction to biological mass spectrometry: Determining identity and species of origin of two proteins

We describe a laboratory exercise that is designed to give advanced undergraduate students in analytical chemistry a meaningful introduction to biological mass spectrometry. We ask the students to solve a mystery: given two proteins, what are they, and from which animals do they originate? This exercise involves use of two mass spectrometers available in our institution: a fairly basic matrix-assisted laser desorption ionization time-of-flight (MALDI–TOF) unit and an electrospray ionization (ESI) ion-trap unit. Our exercise can be completed in two days (including analysis) and provides several interesting and educational surprises. The students, in small groups, are introduced to total mass measurement with ESI, proceed to peptide mass mapping with MALDI–TOF, and finally explore sequence information with ion-trap tandem (fragmentation) mass spectrometry. Even in the most advanced phase, we guide the students, but by this time they usually have their own ideas as to what avenues to pursue. We find that our students become excited after they solve the "mystery"of these proteins, and they receive enough education in the process to be able to join a research project involving biological mass spectrometry