Identifying proteins by mass spectrometry requires breaking the proteins down to small peptides. The questions that follow are aimed at giving you the opportunity to build an intuitive feel for the process.

Problems 1 and 2 may be facilitated by the following tour

1. What kind of peptides do you get when you digest a protein with trypsin? Take some protein and simulate the process.

2. What spectrum of peptides do you get when you digest an organism-worth of proteins with trypsin? The answer should take the form of a graph, with the x-axis indicating the size of the peptide and the y-axis indicating the number of times that size is represented in the tryptic digest of all proteins of a specific organism.

The remaining problems may be facilitated by this second tour

3. How many different sequences of peptides are there of length 1?
Length 2? Length 3? Length 4? Length 5? First calculate the numbers (you don't need a calculator), and then check your calculation through an actual count within BioBIKE.

4. Suppose you sequenced a peptide from the tryptic digest of all proteins of the cyanobacterium Prochlorococcus ss120. You want to know from which specific protein it was derived. How big would this peptide need to be to give you a good shot at uniquely identifying the protein it came from?

5. How much overlap is there in the molecular weights of different peptides? Consider the set of all peptides of length three. How many of them have the same molecular weight? The answer should take the form of a graph, with the x-axis indicating the molecular weight of a peptide and the y-axis indicating the number of times that molecular weight is represented in all peptides 3 amino acids in length.

6. Why are there so many instances of the same molecular weight?