Injection port B [rear port
with green nut]
This port typically operates under splitless
conditions, everything injected reaches the column, at 200 °C with
a Rtx-35 (35% diphenyl 65% polydimethylsiloxane) Integra-guard capillary
column and a head pressure of 17 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 B by pressing
FLOW followed by B 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 until the meter reads ~65. This ensures
that the injection port will be cleared quickly when the purge valve opens.
To use the mass selective detector with this column carefully switch
the internal valve inside the GC oven to the B position (valve knob
set screw points to GC door); change the valve only at oven temperatures
<100 °C. Sample injection should not exceed 2 mL
in this injection port; additionally, the sample concentration should not
exceed 1.0E-04 M. Too much sample will result in poorly shaped (fronted)
peaks or cause damage to the MSD filament.
Injection Port B (green nut) Total Flow Control Knob on Lower Left
Switching
Valve in Position B
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 tracel or traceh (for trace analysis).
Tracel is for compounds that are of high volatility (bp < 200°C
and MW < 350), while traceh is for compounds up to MW 400 and
volatilization temperature of 225 °C. For instructions regarding creating
your own method see Appendix 1.
To prepare the instrument for injection
using the method you just loaded 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 B is initially OFF when using injection
port B. 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, adjust your method
after the run completes. DO NOT select Stop Run in the real time
acquisition window since the purge valve must be reset!
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 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. To return to the original display just click the left mouse button
once in 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.
Output MS or TIC to a text file - to do this you need to know where the data are located in MS ChemStation lingo. Under the Options pull-down menu select Stack. This will show you where the MS ChemStation has located the data from a particular run. See Appendix 3 and 4 for more details.
register objects are prior to colons
You can use this information in a macro called _TAB to output the data in text file format. The syntax of the _TAB command is important to follow and is appended at the end of this instruction set. Two examples of _TAB commands are shown below to help you.
Example 1 (mass spectrum): _TAB ,"c:\temp\pjcmpd1.txt",Y,,
The above example takes the mass spectral data found in register Y (indicated by STACK) and outputs it to a text file named pjcmpd1.txt in the temp directory. The default object is X.
Example 2 (TIC): _TAB , "c:\temp\pjtic1.txt",R0,,
This example takes the total ion chromatogram found in register R0 (indicated by STACK) and outputs it to a text file named pjtic1.txt in the temp directory.
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Appendix 1: Creating a Splitless 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 tracel or traceh 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 appropriated 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 should remain at 250 °C, but you can change
injection port B. Splitless injections donít need as high a temperature
setting as split injections; somewhere in the 150-225 °C range is usually
adequate. 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. Make sure that you include a cooldown line in the temperature
program so the oven is ready for the next injection. The Injection Information
dialog window contains the purge commands for ports A and B. These
values make the split or splitless injections. The only values you may
need to change for port B is the time on and time off; time on should be
less than one minute into the run and the time off should be set to occur
during the cooldown segment of the temperature program. The default purge
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 = 0.67 min, time off = 18.00 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 values 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.
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Appendix 2: Purge flow rate settings
Use the graph below to assist you in setting the split vent flow rate. With the 40 meter x 0.25 mm column and a head pressure of 17 PSIG, the column flow rate is roughly 0.85 mL/min. You can adjust the flow out the split vent using the TOTAL FLOW control knob. Adjust the knob until the meter reads the flow value associated with the split flow rate 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 50 does not mean the flow out the split vent is 50 mL/min.
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Appendix 3: ChemStation Syntax for
_TAB command
_TAB [keyword] [,"filename"] ,MS object [,data range] [,abundance value]
_TAB [keyword] [,"filename"] ,GC/MS object [,data range]
Displays information about the current data file, the contents of a variable, or the current integration events for the ChemStation integrator. This is an overloaded version of the TABULATE command.
keyword
RESULTS A keyword to specify the integration or library search results associated with the object in the specified variable.
PERCENT A keyword to specify percent results when parameter 3 is a GC/MS object. If Sort by Signal is selected on the Percent Report Options dialog box, the specified variable must contain an integrated chromatogram. If Sort by Retention Time is selected, an integration set must exist (see ADDPEAKS). This keyword option may be eliminated in future software revisions; its use is not recommended.
"filename"
The destination file for the tabulation. The default is the null string.
MS object / GC/MS object
The choice of parameter 3 determines whether _TAB accepts four or five parameters. If parameter 3 specifies a variable containing spectral data (MS object), then an abundance value may be specified as parameter 5. If parameter 3 is a GC/MS object, the command has only four parameters.
data range
The range of data to be tabulated. This parameter is relevant only if no keyword is specified in parameter 1. For MS object, the default is the full mass spectral range. For GC/MS object, the default is the full chromatographic retention time range.
abundance value
This parameter is available only when mass spectral data are specified in parameter 3. Specifies the minimum abundance a data point must have to be included in the tabulation.
0 all data points included (default)
>0 - <1 a percent abundance of the maximum abundance
>=1 absolute abundance
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Appendix 4: LabVIEW mschemstation_parse
and EXCEL
This VI takes the text file output from the MS ChemStation _TAB command and parses it into a text file than can be read by EXCEL, sorted and plotted according to the users wishes.
Instructions:
Opening the newly created file with EXCEL
EXCEL will open the text file output from the LabVIEW VI.