Today I'm working on processing the data from my sample analysis. The samples have all been run through the UPLC-MS-MS machine and now I am looking over the numbers the machine came up with. It works by first shooting the samples through a filter then a chrotography column. In the column, the sample is under extremely high pressure, up to 10000psi. As the samples go through the column, the smaller molecules shoot through faster, and the larger molecules take more time to go through. As the sample comes out of the other end of the chromatography column, the fluid in front is composed of the smallest molecules, and the fluid at the end is the largest molecules.
The sample then goes into the tandem mass spectrometers. This instrument puts the molecules under a negative current, which rips off an atom of hydrogen and converts the molecule into an ion. The ions are then fired through a reaction chamber which exposes the molecules to four strong opposing energy fields. These energy fields tear the molecules apart into measurable chunks, and identifies which molecule is which based on mass of the pieces each one is torn into.
Then I get chromatograms which are like wavy lines that look like hills and mountains. I have to use a program to calculate the area of the main peak or hill, compared to the size of a standard peak. The ratio between the two peaks area's yields the concentration of that particular compound within the total sample. Then I have the approximate level of toxin (x,y,z) within the sample, which can be related back to the level of that toxin found in the fish fillet, which can then be related back to the level of that toxin found in other fish from the same location, and then the toxin levels within the fish fillets can be compared to the toxin levels in the water in that location, and a good estimate of the concentration of that toxin in that location can be calculated. So far it seems there are some very pure areas of the nile river, but also some very toxic ones.
Friday, April 23, 2010
Thursday, March 25, 2010
Örebro Movie 'Planet Campus'
This entertaining video shows some of the buildings and locations in Örebro University.
Sunday, March 21, 2010
Thursday, March 18, 2010
Research Video Update 2
Here is the second half of the research video.
1.Second Extraction
A.Repeat steps C-H on residual homogenate, then proceed to part 3
2.Concentration
A.Combine the extracts (appx. 8ml) Evaporate combined extracts to 2ml using N2
3.Purification/Clean-up
A.Add 1ml n-hexan. Shake for 30 seconds. Remove the hexane phase (top) with a pipet, repeat n-hexan wash twice more
B.Transfer the AcN-phase to pre-washed 15 ml PP-tube with 50mg ENVI-Carb and 100uL glacial acetic acid. Shake for 30 seconds
C.Evaporate to less than 1ml (including ENVI-Carb) using N2
D.During step C spike LC-vials with Recovery Standard (RS) consisting of 10uL kolv 68, 10uL kolv 251, and 5uL kolv 216
E.Filter the extracts through pre-washed 0.2um cellulose filters into 1 ml LC-vials
4.Final Concentration & Preparation
A.Evaporate to 200uL with N2 then add 300uL 2mM NH4Ac (aq).
B.If samples become cloudy, centrifuge at 9000g for 30 minutes
C.Sample is now ready for UPLC-MS-MS analysis
1.Second Extraction
A.Repeat steps C-H on residual homogenate, then proceed to part 3
2.Concentration
A.Combine the extracts (appx. 8ml) Evaporate combined extracts to 2ml using N2
3.Purification/Clean-up
A.Add 1ml n-hexan. Shake for 30 seconds. Remove the hexane phase (top) with a pipet, repeat n-hexan wash twice more
B.Transfer the AcN-phase to pre-washed 15 ml PP-tube with 50mg ENVI-Carb and 100uL glacial acetic acid. Shake for 30 seconds
C.Evaporate to less than 1ml (including ENVI-Carb) using N2
D.During step C spike LC-vials with Recovery Standard (RS) consisting of 10uL kolv 68, 10uL kolv 251, and 5uL kolv 216
E.Filter the extracts through pre-washed 0.2um cellulose filters into 1 ml LC-vials
4.Final Concentration & Preparation
A.Evaporate to 200uL with N2 then add 300uL 2mM NH4Ac (aq).
B.If samples become cloudy, centrifuge at 9000g for 30 minutes
C.Sample is now ready for UPLC-MS-MS analysis
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