Date of Graduation

Fall 2014

Document Type

Honors Research Project

Degree Name

<-- Please Select One -->

Research Sponsor

Chrys Wesdemiotis

First Reader

Dr. Michael Konopka

Second Reader

Dr. Matthew Panzner


In mass spectrometry, a compound is taken and converted into a gas-phase ion by an electrical charge (Balogh, 2009). From these ions, a chart is then created that displays the mass to charge ratio, which is able to then be analyzed to find out the charge of the ions, as well as the mass of the compound (Balogh, 2009). One specific type of mass spectrometry there is available is known as a fragmentation spectrometry. In fragmentation spectrometry, the molecule is not only ionized and analyzed, but fragmented parts that are formed into ions are also ionized and analyzed. This is what the project will entail. There are two specific ways in which molecules will be analyzed 1. Electron Transfer Dissociation (ETD) and 2. Collisionally Activated Dissociation (CAD). The two provide the peaks of fragmented ions of a molecule, but ETD fragmentation will actually form slightly different fractions of the same molecule than the CAD fragmentation, which will give different results based on the peaks given (Wesdemiotis, 2012). The purpose of this project will be to take an ETD and CAD of several molecular compounds in attempt to figure out the mechanism of fragmentation from both of the dissociation methods. In order to do this, a group of several known molecules will be analyzed by taking them into an electrospray mass spectrometer and running both ETD and CAD fragmentations on them. One of the primary peaks (a peak that is obtained from a non-fragmented molecule) will be analyzed closely in order to look at the fragmented peaks that are close to it and find the structure of the fragmentations. These structures will be found by taking a look at each molecule, proposing various places where fragmentation can occur due to bonding properties and sterics, and testing them out mathematically in order to find out the mechanism of fragmentation that shows up in the experimental results. There are a couple of issues that may happen based on this experiment. One limitation on the experiment is that the mechanism of the fragmentation is not known, so it will take up a decent amount of time to find out the mechanism in which the fragmentation takes place. It will take multiple proposed mechanisms, as well as calculations, to be able to find the actual mechanisms of both the ETD and CAD fragmentations, which will limit the amount of molecules that can be done. Another issue in particular is that not every peak that is given in the spectrometry will have to do with the molecule in itself. Mass spectrometers are incredibly sensitive machines, and any sort of addition of molecules, such as a carbon oxygen loss or addition, to the original compound will not only give peaks that will give incorrect values, but it will take up incessant amounts of time in calculations and proposed mechanisms to show that these are not actually part of the fragmented compounds. This will lessen the time available to obtain the actual fragmented mechanisms, and will lessen the amount of results obtained within the allotted time. One final limitation is the possibility of impurities within the machine. As said before, mass spectrometers are incredibly sensitive machines, so any impurity that is left in the machine will cause a change in the data received. The machine will need cleaned in order to obtain proper results, which will take valuable time away from the process of the experimentation, which will allow fewer results to be received in the experiment.

There are many things that can be gleaned from this project. One of the things learned will be the differences in how fragmentation works between the two fragmentation methods. Another will be how to propose a mechanism of diffraction, as well as calculate if this diffraction occurs within either method. Once the correct mechanism is found, it may also show the properties of fragmentation patterns and where fragmentations will occur as well. There are several benefits from understanding fragmentation: One, it will give information of how bonding works in a molecule, and where bonds can break based on the structure of a molecule. Second, this may be able to be used as a precursor to further experimentation with fragmentation, and help in easing the calculations of further research in the field of ETD and CAD. Finally, if the properties of bonds can be further understood based on this, a better understanding of reactions may also be understood by being able to know which bonds will possibly react within a reaction.


Figures were not able to be placed with the project due to formatting. A second file will need to be added to be able to put in the figures.