MAAD Scientist Technologies

Learn · Mass spectrometry

The Mass Spectrometer

Your protein is 183 Da too heavy. Your “leucine” might be isoleucine. And 250 of your 5,000 features are noise.

Best full screen: the text is small otherwise. Click the game first, then use the arrow keys to choose, Enter to confirm and Esc to leave. It needs a keyboard, and takes a few seconds to load. Open it in its own tab.

What you do

You read spectra. Five tracks of them, each a little less forgiving than the last.

  1. Warm-up. Isotope patterns, charge states, and the fingerprint a protein leaves when it is cut into pieces.
  2. Your prep. The mass of your purified protein doesn’t match its sequence. By how much, and what did that to it?
  3. Proteomics. Thousands of proteins at once. Which identifications are real?
  4. Metabolomics. Thousands of peaks for a few hundred real molecules.
  5. The paper. What you did to the data between the instrument and the figure.

What you find out

  • How a mass that is off by a specific amount tells you exactly what happened to your protein, down to which reagent in your buffer did it.
  • Why a deliberately wrong database tells you how many of your right answers are wrong.
  • Where the keratin came from. (It was you.)
  • Why one molecule shows up as many peaks, and why two different molecules can show up as one.
  • Why running thousands of tests guarantees some false discoveries, and what to do about it.
  • How a result can track the day the samples were processed instead of the thing you were studying.

Where the science comes from

The mass shifts are standard reference values, and each trap in the game is drawn from a published paper that documented it. Peak heights, the generated proteins and the noise are the game’s own.