The Flowing Afterglow

Aside from my main project, I have been helping get another mass spectrometer in the lab up and running: the flowing afterglow.  This instrument allows us to conduct reactions in the flow tube to produce ions using volatile compounds.  In addition, temperature and pressure can be controlled in the instrument to create an atmospheric environment for these reactions.

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Learning about SEQUEST

The program that we use in order to identify proteins is called SEQUEST.  When I first started working in the lab, I ran spectra through this program by changing various parameters and then watching it work, without really understanding the process that it takes to come up with the best peptide/protein matches for the sample.  Now I understand the modifications of the program help get the most accurate values possible.

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Coming Around the Final Turn

Greetings once more from the ISC. Things in the lab have been moving forward, if rather slowly in some cases. We have been facing the inevitable issue of bottle-necking in terms of making use of the two magnets we have in our lab, for there are multiple projects which need to collect data. On top of that, we have recently discovered that the lift which allows us the vary the depths at which we are measuring during a single experiment has not been moving in accordance to the distances it is given in the software, which has slowed down all data collection as we work to correct or at  least better understand the issue. Nonetheless work progresses on the paint cleaning front. The samples which were assigned the isopropanol treatments have continued to be treated with the swab and gel techniques respectively. The double peak phenomenon exhibited by the sample which is swabbed with isopropanol could potentially be a result of isopropanol’s rapid evaporation rate, causing a peak to be observed where paint had swelled as normal, and another peak due to some isopropanol which has been trapped in the sample. The samples will continue to be treated on a regular basis and perhaps the next measurement will bring even more insight about the two peaks exhibited by the plain isopropanol.

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Long time, no see!

It’s been quite a while since I’ve been able to update my progress due to some unforeseen issues.  On the 19th of June, William and Mary mistakenly cut the power to the Integrated Science Center as a part of a scheduled campus-wide power outage.  When the power was reintroduced to the buildings, the instruments, which previously were on, turned back on immediately and improperly.  This blew both power supplies to the mass spectrometer, which can only be replaced by an outside repairperson.  During the three week period of waiting for him to find replacement parts and travel from North Carolina to Williamsburg, I did a lot of research for our kinetic method projects, namely condensing information about experimentally and theoretically retrieved proton affinity values for glycine.  In addition, we worked on our flowing afterglow mass spectrometer, which needed some plumbing adjustments and a change to the software before being able to produce scans.

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Another day, another test…

Time might be winding down, but there is still much to be done, so much so that late-night chemistry is now a thing. As usual, my last week comprised mostly of running electrochemistry tests on my primary complex, obtaining data that is frustratingly close to being publishable. I have solved the decomposition issue, but the major obstacle now is a poor connection between the electrode leads and the clips connecting the wires to the potentiostat. Sometimes, the instrument does not register that the electrodes are hooked up, resulting in a flatline CV of the reference electrode instead of a useful CV. Every time electricity runs through the complex after acid addition, it seems to decompose, meaning that after each experiment, I am left with only a couple of CV points rather than four or five due to the poor connection. Hopefully this becomes a less recurring theme because we cleaned the electrode leads on Friday, which should improve the connection. Work on the other ligand/complex pairs varies between crystallization attempts, synthesis of either the ligand or complex, or electrochemistry tests. Based on the early results of a few complexes, our paper topic might revolve around a different characteristic of the complexes than we previously thought, which is promising and exciting. This summer has been an enjoyable one, and hopefully what I acquire now I can apply in the future.