Thin Layer Chromatography
Gas Chromatography-Mass Spectrometry
Chromatography-Mass Spectrometry (GC-MS)
will not not use the GC-MS instrument, they will frequently have to use
GC-MS data to analyze chemical compounds.
Preparation of your sample for GC-MS:
All GC-MS samples should be dilute! For most liquid samples, prepare a 10% v/v solution of your sample in methylene chloride for GC/MS. See your lab instructor if your sample is not soluble in methylene chloride. Using a disposable glass pipet, measure 8 drops of your sample into a small test tube. Use another disposable glass pipet to add approximately 2 mL methylene chloride to the test tube. Transfer this solution to a GC-MS vial, and give your sample to the student lab assistant.
If you have a solid, dissolve 10-50 mg of your compound in 3mL methylene chloride.. Please consult your organic solubility tests to determine if your unknowns are soluble in methylene chloride BEFORE creating your GC-MS sample. (If your unknown does not dissolve in the methylene chloride, consult your instructor.) Mix well and transfer the solution into a GC/MS vial, using a disposable glass pipet.
Directions for Retrieving GC-MS data:
- 1. Log on to any one of the four computers on the same table with the printer in SCI-230.
- Starting from the Windows button on the bottom left-hand side of the screen, type “\\ntm” in the rectangular white box and hit Enter. (Make sure to use the correct ‘backslashes’ in your search.)
- From the file folders on the ntm server, navigate to the Chemistry/211 GC-MS folder.
- Locate your data by opening the following folders: your semester folder, your lab day folder, and then the desired experiment folder, for example, 211F11/Monday/COMPNUC for the competing nucleophiles experiment.
- Drag your data file name folder to the desktop.
- Open the “Data Analysis” program shortcut on the desktop (or go to all programs/MSD ChemStation/Data Analysis.) Wait for the program to load.
- From the File menu, select Load Data File.
- On the “Select Data File...” dialog box, click “Change Path”. Select Desktop in the “Browse for Folder” dialog box. Click OK.
- Highlight your data file name and click OK. This will bring your GC to the screen.
- If the GC for your sample shows a black background and no peaks, do the following. Click on the “Edit Colors” icon, which is a rectangle of four colors. From the drop-down menu, choose “Default Theme” and save your choice. (You will only have to do this once. The colors will be saved for the next time you open the program.)
- From the menu bar, select Chromatogram and then select Percent Report. To copy your percent report data table into your e-lab, highlight your Area Percent Report’s data table and copy (ctrl-C) and paste (ctrl-V) the data table into your e-lab.
- To copy your GC into your e-lab, select “Copy Windows...” from Tools in the menu bar. In the Input window, enter “2” and click OK to copy your GC. Then, paste (ctrl-V) your GC into your e-lab.**
- To obtain a mass spectrum of any compound in your GC, put the cursor directly over the middle of the GC peak and double click with the right mouse button. [It’s recommended that you follow the instructions below for enlarging each GC peak before obtaining its mass spectrum.]
- You will need to remove the masses in your mass spectrum that come from the compounds which make up the baseline in your GC. To do this, generate the mass spectrum for the GC peak you are interested in. Then, generate the mass spectrum of the baseline to the left or right of the GC peak. Make sure the area you select is completely flat and isn't part of any GC peak. Under Spectrum, in the menu bar at the top of the screen, highlight Subtract. This will generate the mass spectrum for your compound only. It will remove any masses in your spectrum created by the baseline compounds, such as the solvent that you dissolved your sample in.
- Only copy the peaks and mass spectra that are of interest to you. To copy either any expanded region of your GC or expanded MS for your e-lab: find Tools in the menu bar and select Copy Window…. In the Input window, type 2 for your GC of the expanded peak or type 1 for your MS on the screen. Open the document you want to paste your GC or MS in and under Edit, select Paste or type ctrl-V.
- For the Competing Nucleophiles lab, you should copy the mass spectra of the 3 largest peaks on the GC into your e-lab. Two of these spectra should be your 2 expected products. You may also see a peak from unreacted starting material. (Your instructor may modify this assignment.)
- When finished, go to File and select Exit.
- Remember to log off when you are finished.
**TO ENLARGE...a section/peak of either the GC or the MS, use the left mouse button to drag a box around the desired area. You must include the tip of the peak and the x-axis scale. To return to the full spectrum, double click with the left mouse button anywhere on the GC or MS.)
Printable Directions for Retrieving GC-MS data