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.
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.
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.
Well, it seems that somehow I’ve managed to lose the earlier post I made this year, so I’ll start from the beginning.
After reading the first paper to begin my preparation for my study. My jaw dropped to the ground. My brain is doing jumping jacks trying to understand all the dense information carefully placed in published papers. After two weeks of reading papers to prepare for the lab aspect of the project, I now go Germany to make everything work. I am here in Frankfurt, arrived this morning and I will travel down to Freiburg by train to start work in the afternoon. WOOO. I will be learning, taking notes and setting up my experiment. It finally all comes together. It is really thrilling to see all that I have learned in class in action in past papers. From the moment I learned about epigenetics in Molecular Biology, I fell in love. A big shout out to all my professors at W&M for their inspiring lectures!!!