1. Click anywhere to go on to the next slide
What distribution of peptides result from digesting proteins with trypsin?
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2. Teach BioBIKE how to be trypsin.

3. Trypsin is a digestive enzyme. Digestion here pertaining to proteins
Trypsin is a digestive enzyme. Digestion here pertaining to proteins. So we’ll probably want one of those proteins I keep hearing about.

4. Or rather, we’d like the sequence of a protein
Or rather, we’d like the sequence of a protein. Perhaps something in our favorite cyanobacterium, ss120.

5. Here’s a protein in ss120: p-pro0047
Here’s a protein in ss120: p-pro Type it in the box and click “Execute” to evaluate the expression and see the sequence in the lower frame.

6. Ok. There it is, in all its glory. Or rather 200aa of its glory
Ok. There it is, in all its glory. Or rather 200aa of its glory. But that is neither here nor there. Select “Split” to begin thinking like an enzyme.

7. It looks like BioBIKE would appreciate a string here
It looks like BioBIKE would appreciate a string here. Fair enough, let’s give it one…

8. Click in the SPLIT field.

9. Over in our sequence-calling node, select “Cut” to cut this function…

10. … and paste it into the SPLIT function.

11. I’m not sure what this slide illustrates. Take a moment to ponder life.

12. Done and done. Let’s give SPLIT a little guidance by telling it where to cut the string.

14. Trypsin cuts peptides on the carboxyl side of every arginine and lysine (R and K, respectively). Thus, “K.” Try executing your SPLIT command to see this in action.

15. But we need to tell BioBIKE two places to cut
But we need to tell BioBIKE two places to cut. A list may be of assistance here.

19. “K” and “R. ” Robot trypsin will cut after every Lysine and Arginine
“K” and “R.” Robot trypsin will cut after every Lysine and Arginine. Hit execute to see what this looks like. Seems pretty variable… I wonder how long each fragment is? Choose “Surround with” and …

20. … LENGTHS-OF to evaluate the length of each fragment
… LENGTHS-OF to evaluate the length of each fragment. Don’t forget we want the plural statement, and not the one directly above it.

21. Hit “Execute.”

22. And there they are. The length of each fragment of the protein p-pro0047 as digested by Trypsin. Do the numbers make sense? You can check by executing only the SPLIT function.

23. Now that we digested a single protein, let’s do all the proteins in an organism. Erase p-pro0047 and choose “PROTEINS-OF” from the GENOME menu.

24. Execute LENGTHS-OF again to display the lengths of all the proteins in ss120.

25. Check the numbers again
Check the numbers again. If these seemed a little odd to you, you’d be right. Check the sequences again (hit SPLIT).

26. Double parentheses! BioBIKE is actually returning lengths of lists of proteins, essentially the number of fragments per protein. What we want are lengths of fragments, regardless of protein.

27. We can take care of this headache with the SIMPLIFY-LIST function, which goes around your SPLIT node.

29. No more ((double parentheses))!

31. Now that it works, we want to package the procedure so that we never have to think about it again. Select “collapse” from the SIMPLIFY-LIST node.

32. Add “DEFINE-FUNCTION.” It’s up in the DEFINITION menu.

33. Give it a catchy name.

34. And a helpful summary

35. 2 1 3
1) If you ever forget exactly what type of input this function needs, this’ll tell you. 2) Copy your SIMPLIFY-LIST collapsed node and 3) paste it into the body field.

37. Going back to digesting a single protein, we make the connection between function and input and evaluation. Delete the PROTEINS-OF node.

39. And type “proteins,” which is the variable we asked trypsin-digest-of to look for in the first place.

40. Executing DEFINE-FUNCTION adds our function to BioBIKE.

41. Check it out. No, seriously. Check it out.

42. 2 1

45. Much less cluttered.