Injection port A [front port
with black nut]
This port operates under split flow conditions
(80:1) at 250 °C with a Rtx-5 (5% diphenyl 95% polydimethylsiloxane)
Integra-guard capillary column and a head pressure of 14 PSIG. The guard
column length is 10 m followed by an analytical column having the following
dimensions: 30-m x 0.25-mm x 0.25-mm
film thickness. Check the total flow of gas to injection port A by pressing
FLOW followed by A on the GC keypad. If the meter reads something
other than ~65, make the appropriate change in the flow rate by turning
the TOTAL FLOW control knob, on Injection port A, until the meter
reads ~65. The split ratio is now roughly 80:1. If you find that your sample
is too dilute or too concentrated after injection, you may adjust the split
ratio to compensate. See Appendix 1 for instructions. To use the mass selective
detector with this column the internal valve inside the GC oven must be
in the A position (valve knob set screw points left toward MSD).
This is the default position of the valve! Do not change it. Sample injection
should not exceed 5 mL
in this injection port; additionally, the sample concentration should not
exceed 1.0E-02 M (approximate concentration for NMR analysis). Too much
sample will result in poorly shaped (fronted) peaks or cause damage to
the MSD filament.
Injection Port A (black nut) Total Flow Control Knob on Lower Left
Switching
Valve in Position A
The GC and MSD are controlled by a PC running MS ChemStation software. This package permits instrument control, data collection, and data processing.
Control-Data Collection. The control
and data collection software utilities (GC/MS Top) are found under the
5970-Instrument-1 group in the Windows program manager. Once started you
will see a window labeled Top. Load a method by pulling down the Methods
menu and selecting Load.... Scroll through the method files
and select either genlow or genhigh. Genlow is for
compounds that are typical organics (bp < 220 °C and MW < 340),
while genhigh is for compounds up to MW 500 and volatilization temperature
of 270 °C. For instructions regarding creating your own method see
Appendix 2.
To prepare the instrument for injection
using the above method select Main Panel under the DataAcquisition
pull-down menu. This will download all the parameters from the method to
the GC and MSD; a new dialogue window "Acquisition" will
appear. To inject a sample select Inject under the Data
pull down menu. Enter the appropriate filename (8 characters maximum)
and sample identification information in the boxes, then click OK. The
software will check for system readiness. It is important to check that
PURGE A is ON when using injection port A. If it is not, change it using
the GC keypad. Follow the directions and inject your sample. Press START
on the GC panel as soon as you have finished injecting your sample. This
signals the software to begin the data collection protocols and a real
time acquisition window is displayed. Never override the solvent delay
unless an emergency situation arises. If all your compounds elute prior
to the end of the run, select Stop Run in the real time acquisition
window to conserve analysis time.
Data Analysis.
For data analysis use the StandAlone Data Analysis package. This way you
can process data during analysis runs! Find the StandAlone Data Analysis
icon in the 5970-Instrument-1 group of the Windows program manager. After
the program loads you can process any data file you wish or take a ìsnap-shotî
of the one currently running. To load a file for analysis pull down under
File and select Load. Find the file in the
dialog box and click OK. The total ion chromatogram (TIC) will be loaded
into register R0 and displayed at the top of the window. Double click
on a peak using the right mouse button to show the mass spectrum
for a particular time point. If you wish to average the mass spectra over
a certain time range, just hold the right mouse button down and drag over
the appropriate time span in the TIC. You can expand any scale (in either
the TIC or MS) by holding down the left mouse button and dragging
the outline of a box in the window. To return to the original display just
click the left mouse button once in the appropriate window. To take a ìsnap-shotî
of a current run select Take Snapshot from the File
pull-down menu. Process accordingly. To print the TIC, MS, or specify a
window to print, select Print from the File
pull-down menu. Select the appropriate response in the dialog box that
appears. Remember that any zooming you do will be printed as such unless
you reset prior to printing!
To obtain peak widths and areas for peaks
in the TIC you have two options: A) Pull down Chromatogram
and select Integrate. This will evaluate all the peaks above
a given reference level established in your acquisition method. B) Type
GET n on the command line, where n is an integer number. This will
integrate the n peaks having the highest signal in the TIC and display
the corresponding mass spectra. After either option select List
Results under the Chromatogram pull-down menu. A new
window with the integration results is displayed. Copy these values to
the clipboard for pasting into other documents or print them.
Library Matching - to see if a mass spectrum matches one currently in the NIST library, just display the mass spectrum and double click the RIGHT mouse button in the window containing the mass spectrum. The search results will be displayed and you have the option to print them. Scroll through the search results window to find the database compound that most closely matches your mass spectrum. Remember, not all the worldís compounds or their derivatives are in the database!
Displaying multiple mass spectra - to display multiple mass spectra you must use a few macro commands. First, display two sequential mass spectra by clicking in the TIC with the right mouse button. Then type MERGE on the command line at the bottom of the window followed by a return. This will orient the two spectra in one window. Type DRAW on the command line and you will see them displayed. To add another mass spectrum, just display it as usual by selecting the spot in the TIC and clicking the RIGHT mouse button. Now repeat the MERGE and DRAW commands. Once you have decided upon the exact number of spectra you wish to display you have one more option. You can plot them all with the same Y-axis. To do this enter NORMALIZE 100 on the command line. This will normalize each spectrum to its base peak (ion fragment with the highest signal) and the 100 indicates the maximum value on the y-axis scale. Enter the DRAW command one last time to update the display.
Appendix 1: Adjusting the Split Ratio
Use the graph below to assist you in setting the split ratio appropriately. With the 40 meter x 0.25 mm column and a head pressure of 14 PSIG, the column flow rate is roughly 0.86 mL/min. Set the total flow rate using the TOTAL FLOW control knob. Adjust the knob until the GC meter reads the flow value associated with the split ratio desired. Please note that the electronic flow meter DOES NOT display the split vent flow rate; it only approximates it! Thus, a meter reading of 40 does not mean the flow out the split vent is 40 mL/min.
Appendix 2: Creating a Split Analysis Method
Method Creation. The control and
data collection software utilities (GC/MS Top) are found under the 5970-Instrument-1
group in the Windows program manager. Once started you will see a window
labeled Top. Load either the genlow or genhigh
method depending on the sample type to analyze. Modify the existing method
to create a new one by pulling down the Methods menu and
selecting Edit Entire Method. Check all three boxes to edit.
Make the appropriate changes in the ensuing dialogue boxes and save your
file at the end with a new name (remember it must be 8 or fewer characters
long).
A few important notes regarding the dialogue boxes are contained in this section. Enter comments regarding the method you are creating and your identity in the Method Information window. You should save a copy of the method with the data and only the Data Acquisition box should be checked as a method section to run. In the Normal Scan Acquisition window change only the solvent delay, mass range, and plot parameters. Keep in mind that the number of scans per unit time depends on the mass range scanned. As the scan range increases, the number of scans will decrease. Additionally, do not make the solvent delay too short!! The next window is the Temperature Information window. Injection port A temperature may be changed, but injection port B should stay at 200 °C and detector B at 280 °C. The real method creativity is associated with the oven program on the right hand side of the window. The maximum rate of heating or cooling is 70 °C/minute and the maximum temperature the oven should reach is 300 °C. A graphical display shows the run time and temperature program you enter. DO NOT change anything in the Injection Information dialog window; it is preset for split injections. The settings should read as follows: Injector port A: initial value ON, time on = 0.00 min, time off = 0.00 min; Injector port B: initial value OFF, time on = 0.00 min, time off = 0.00 min. If these are not set appropriately then the system will not function properly during injection and analysis. NOTE: when the purge time on and time off are set to zero the purge valve does not change from the initial conditions. The remainder of the dialog windows can be ignored. Remember to save the method with a new name; avoid overwriting the old method and reeking havoc with the system.