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1 1 Gas Chromatography/Mass Spectroscopy (GC/MS/MS) Background Information Instructions for the Operation of the Varian CP-3800 Gas Chromatograph/ Varian Saturn 2200 GC/MS/MS See the Cary Eclipse Software Operation Manual reference on page 49. Gas Chromatography/Mass Spectroscopy (GC/MS/MS) Background Information Gas chromatography (GC) is a method used to help identify a mixture of compounds by separating compounds according to each compound s retention time. Compounds with a lower molecular weight will elute out earlier than compounds with higher molecular weights due to differences in boiling points. Smaller structures have lower boiling points and will thus elute faster than those with higher boiling points. It then follows that the compounds with the lower boiling points will have shorter retention times (Petrie). Another advantage of GC is that it can be used to determine the purity of compounds. By looking for additional peaks in a sample that are not present in the pure compound, one can gain knowledge about purity. Peak areas of additional peaks can provide an indication of the degree of contamination (Skoog 716). Factors other than the boiling points of compounds will also affect separation. Other factors that determine the separation are: the polarity and physical size of the molecules (for example branching), the column type (i.e. polar or nonpolar), and the number of theoretical plates (Petrie). The polarity of compounds should be considered because polar compounds will have a longer elution time on a polar column (i.e. the stationary phase) while a nonpolar compound will elute in shorter times (Skoog 714). The mobile phase flow rate (how fast the gas is carrying the compounds through) also affects the appearance of peaks on the chromatogram (Skoog 683). If the flow is too fast, peaks may not separate out as well, however, if the flow is too slow, band broadening may occur. Column efficiency (comprised of plate height and the number of theoretical plates) is another aspect that must be taken into account. The smaller the height equivalent to a theoretical plate (the more theoretical plates present) the more efficient the column (Skoog 681). In the actual process of running a gas chromatograph, a sample is run by using a syringe to inject your compound into the injector port, which leads to a column. A carrier gas (in our case helium) is utilized in order to carry the sample on to the column. The various compounds in the sample will separate (according the factors previously mentioned) and result in the appearance of peaks at different locations on your chromatogram (Zubrick 251). Compounds are identified through their chemical compositions which can be obtained by a variety of means. Mass spectroscopy is one of the chemist s tools in their arsenal. Through mass spectroscopy (MS), one can determine the molecular weight, molecular formula, and the functional groups present on a compound (Skoog 524). The molecular weight can be determined by identifying the molecular ion peak (Skoog 525). Looking at the mass to charge ratio (m/z) and the distribution of isotopes, one is able to determine an average mass for a compound. The mass contribution of each isotope is

2 determined by each isotope s mass and relative abundance. Adding all of the isotopes mass contributions will then result in an average mass for the compound (Robinson 723). The molecular formula for a compound can then be ascertained from the relative peak heights of the isotopes (Skoog 525). Peak areas and heights can also be useful because they can indicate the concentration of various components present in the sample (Skoog ). When looking at mass spectra, the majority of peaks that appear are attributed to fragments; these fragments are pieces of the original compound that have separated from the compound. The appearance of these fragments makes interpretation slightly more difficult, which is why the use of a library can become advantageous. By comparing your sample to knowns, a positive identification is possible (Skoog 524). So how does mass spectroscopy work? Upon passing through the column the particles continue on to the mass spectrometer where the sample is bombarded by highenergy electrons (Silberberg 54). These electrons collide with the atoms in the sample and, as a result, knock an electron off of the sample s atoms, inducing a positively charged particle (Silberberg 54). The particles are then separated by a variety of means depending upon the type of mass spectrometer used. For example, in an ion trap mass spectrometer (which we use in our labs) the particles are deflected depending upon their mass/charge ratio (Skoog ). A detector determines the particles relative positions and abundances which can then be used to determine the identity of the compound (Silberberg 54). The largest peak in the spectrum is called the base peak. The heights of all the additional peaks in the spectrum are then measured as a percent relative to the base peak (Skoog 499). The main advantage of interfacing a gas chromatograph with a mass spectrometer is its efficiency. With combined instrumentation, only one sample needs to be prepared. This saves on both time and materials. The physical bench space taken up is minimized as well. The GC/MS/MS allows one to obtain more detailed information about unknown compounds faster and more easily than the instruments separately. Combining these technologies allows one to analyze more complex compounds faster than a GC, MS, or GC/MS (Skoog 531). 2

3 3 Varian CP-3800 Gas Chromatograph Varian Saturn 2200 GC/MS/MS Before starting a method, you must make sure to check what the maximum allowable temperature is for the column that you are using. You do not want to set up a method with a temperature that exceeds the specifications. For most undergraduates purposes, you will not need to create a new method. The instructor should specify which method is appropriate for your use. If in doubt, ask. Also important, for running samples you only have to set up the method on the computer. DO NOT touch any of the buttons on the instrument itself! Opening/Editing Methods

4 4 When first signing into the computer, a row of buttons will appear on the top of the screen. Click on the View/Edit Methods button. When the Create/Open Method File box appears click Open an Existing Method File OK. o A list of methods will appear; choose the appropriate method as instructed by your professor. o When the method opens, a list of specifications will be shown on the left hand side of the screen Mass Spec Control option will bring up detector control parameters. By double-clicking on MS Method Editor, another screen will appear where you can change some of the specifications for the MS. Most likely, your professor will already establish these. The specifications can be changed or new ones added. Clicking in the box and changing the command (i.e. start time, low mass, ionization mode, etc.) will alter the setup method for that MS. Clicking Add will add a new line of specifications. A box labeled Segment Setpoints will then appear where you can change the scan time, count threshold, emission current, etc GC Control has several subtopics listed beneath it but the main ones you should be concerned with are: Injector, Flow/Pressure, and Column Oven. As with the MS, many of the specification will already be established. Injector The box on the right indicates the injector type. The Front Injector Type should be set for Injector Oven should be On. Injector Coolant should be Off. Enable Coolant At you can change the temperature with the toggle up or down. Coolant Timeout increase or decrease the time with the toggle function. Flow/Pressure Front EFC Type should read: Type 1 (for 1079/1177 Injector). Constant Flow should be On. Column Flow is typically 1.0 ml/min but can be adjusted by toggling up or down. Column Oven Column Oven Coolant toggled Off. Specify the temperature to enable the coolant at by toggling up or down.

5 5 Coolant Timeout can be altered by toggling. Stabilization Time varies but can be adjusted accordingly. If you have edited a method, make sure you save it under a different filename. Running Samples The correct method must be displayed in the following locations: o Method Operations If you accidentally opened the wrong method, click on this button. Click on Pick a Different Method and select the appropriate method. Then click the Method Operations button again View/Edit Method. Quick Start Instrument 1 Status box will appear; you generally do not need to be concerned with this. MS QuickStart-1 box will appear. Fill in Operator Name and Sample Name. Click in the Primary Method field and click the browse button. Select the appropriate method. Follow the same steps for the Folder for Data File Storage field.

6 6 Do NOT click the green Start button yet. The System Control window must be filled out first! o System Control window (seen on page 34) On top of the box, a field should indicate the method. If the correct method is not selected, click on the folder icon immediately to the right and select the appropriate method from the Activate a System Control Method File window. Not Ready will then flash red in the System Control window. During this time, use a solvent with a low boiling point (i.e. acetone) to clean the syringe. Repeat 2-3 times. Clean the syringe with your sample ~2-3 times and discard the waste in the proper container. Once all 3 boxes have the method correct, click Start in the MS Quickstart window. A box titled Generic SampleList will pop up indicating the sample name and sample type. When the new method is activated, the parameters for the method should appear on the screen on the GC/MS instrument itself. When Waiting is flashing in yellow on the System Control window and the Ready light is illuminated on the instrument, prepare for the injection of your sample by slowly pulling the plunger up to draw your sample into the syringe. You should only need ~1-2µL. The syringe is now loaded. With the needle out of the solution, pull the plunger back slightly more until you can see some air in the syringe. This will prevent your sample from being vaporized when you insert the needle but don t quite inject the sample yet. Then, with one smooth motion inject your sample and make sure that you push the 3-pronged start button on the instrument. 3-pronged start button Once all of these steps have been completed, a line at the bottom of the screen should show your method name as being activated. Analysis After the sample has been run, you can view both the MS spectrum and the chromatogram by clicking Spectrum and Chromatogram in the pull down box in the window. Once the chromatogram has been drawn, clicking anywhere on the chromatogram will bring up a window for the MS spectra.

7 7 will take away the toolbar. zooms out of a closer view to take you back to the original chromatogram. zooms in to a closer view. allows you to change the parameters on the plot. In the MS Data Review window, clicking on the button vertically tiles windows, horizontally tiles windows, and windows. cascades the chromatogram and spectral Horizontally is usually the easiest to use because you can view both windows at the same time across the majority of the x and y scaling. To assess peaks, go to the toolbars on the chromatogram and click on Quantitation Integrate Active Plot. A box will appear indicating the peaks and relative area under the peak, as well as the signal to noise ratio. Search o Library Search a Spectrum Select a spectrum from the list on the right. A window will appear with a list of possible matches in order of probability. If you click on the name of a possible spectral match, the complete spectrum, along with that compound s structure will be brought up in a box on the right hand side. This can be compared to your sample spectrum conveniently since both the sample and match will be displayed at the same time. o Library Search by : This allows you to search a library by a specific peak, CAS number, formula, or molecular weight. Opening Saved Data Go to the Review/Process MS Data button on the top toolbar and click on it. A Select Plot(s) window will appear. Choose your file by doubling clicking. The filename will then appear in a box below. Click on it and select the Open File(s) button. Your file should now appear on the screen. Printing

8 8 To print a MS spectrum, select the Print button from the Spectra window. This brings up your spectrum in a new view. In this new window, go to File Print Page. To print a chromatogram, select File, then Print from the Chromatogram box. A window will appear with several printing options. Select the one desired (i.e. Print Active Chromatogram) and a page will appear that was similar in appearance to spectrum previously mentioned. In this new window now displaying your chromatogram, go to File Print Page. Closing Down When you are finished running your samples activate the standby.mth method in the System Control box. The screen on the instrument should indicate that the method has been changed and a line on the bottom window of the computer monitor should also indicate such. Close all of the remaining windows and log off. Turn off the monitor. Print View

9 9 System Control Window Correct method must be selected here Open correct method for System Control field Injection Status Mass spectra will appear here Gas chromatograms will appear here Experiment status

10 10 Results for GC/MS Analysis Hide toolbar Zoom out Print Zoom in

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