Day one of the actual experiment is here!

S1050022So today I finally got the caterpillars! Thanks so much to Rose Franklin in Pennsylvania for shipping them on Saturday so we could get them on time! Here’s a picture of one of our little guys on one of our test plants. Each plant that is in a caterpillar treatment tub was given one caterpillar. They were placed on the plants at 1 this afternoon so we will start sampling the plants at 1 pm tomorrow at the 24 hour mark. It’s interesting working with living creatures. I’ve been working with the plants since last november from when they were just seeds sitting in a fridge, and I’ve become very protective of them. Granted, a lot of that came from me needing the plants to be alive for this week when we are actually running the experiment, so earlier in the summer when some plants started showing signs of distress I got very concerned with their well-being. The caterpillars on the other hand I instantly bonded with, they are so cute! There was only one that I didn’t really like, while I was putting caterpillars onto the plants in the cages the rest I kept in a box. One of the larger caterpillars almost instantly began to eat a smaller caterpillar during the 5 minutes they were without a food source! (I had enough caterpillars so losing one didn’t set us back at all, but caterpillar cannibalism was quite a shock) Once they were on the plants they stopped trying to eat each other! Now all I have to worry about is caterpillars moving from one plant to another, but I am going to be monitoring their movements multiple times a day so if a caterpillar does move to another plant within a tub we will have it recorded. S1050014

Further analysis of current data

Over the past few weeks, I learned more about how to use the mass spectrometer properly. At first I learned how to use the basic functions of the instrument.  Then I learned that when the data looks skewed, I have to search for what I was doing incorrectly. In order to do so, I have to adjust the collision energy as well as the isolation width in order to see certain fragments. Through several trials, I discovered that contamination appears in single MS and not in tandem.  In cases where we find two peaks from the monomer and the fragments, we add analytes to our data.

Learning how to analyze data

The grad student in my lab taught me how to analyze the dissociation of dimers more closely and reasons for our specific experiment. After tuning, I try to adjust the collision energy in order to find certain peaks at a higher ion count. I learned that when I see homodimers form, then the solution at question is dimerizing. I also learned that fragmentation is essential as the solution breaks up, all the fragments should add up to the original compound. Also, if we chose to analyze only two of the fragments, then we would have to look at those two fragments for each dimer. Furthermore, she informed me that compounds that form intramolecular hydrogen bonded rings are satisfied as they are so they do not like to form dimers.

Reading about Mass Spectrometry

During the days of waiting for the mass spectrometer to be fixed, I learned a lot about the purposes for our experiment. Upon reading several articles, I learned that finding the proton affinity of different compounds is crucial as it is one of the most fundamental  properties in chemistry. In addition, dimerizing is a form of non-covalent bonding of two compounds through a hydrogen bond. We only use references that have one basic site so that we know where they protonate. In order to find the relative proton affinity of our analytes, we must know the absolute proton affinity for our references.  These are usually obtained using the equilibrium method.  In my reading, I learned the many different ways to measure proton affinities including equilibrium, the kinetic method, and the bracketing method. As our analytes are non-volatile, we are forced to use the kinetic method.