GCMS reports
You will use the PostRun Analysis software.
Go to Windows "file" menu, select open data file, and browse to your data file to open it.
Explore your data first to decide what to put in the report. This includes integrating each peak and determining the retention time of peaks you are interested in.
Integrate Chromatograph Peaks
For the first peak:
click on the icon for "manual integration of peaks" about
2/3rd's over to the right, with a small hand on it
move the mouse to the left of a GC chromatograph peak
click and hold down the left mouse button and drag the cursor
to the right side of the peak before releasing
from the popup menu, select the way you want it integrated (I
usually use the top, "link point" option)
For the next peak on the GC trace, you must repeat every step
above (starting with clicking on the manual integrate icon)
View mass spectrum for different retention times
on the GC trace, double-click at a given time to see the MS
that was collected at that time. If you click along a flat baseline, you
can see if there were any stray materials entering the MS. You may find a
handful of ions that are present throughout that you may be able to identify as
impurities in your MS.
click on a peak to view the MS. Comparison of beginning, middle, and end will show whether the composition of the peak changed and indicate whether that peak represents a single compound or more than one overlapping compounds. Jot down the retention times of the peaks you are interested in so you can include them on the report.
Create a Report
On the left menu, click on Report to bring up a blank report
page. Use the icons at the top left of the screen to add particular items
to the report. For each, click the icon and then drag a box for the
placement and size of this item on the report. You will then customize the
info using the popup "properties" window for that item.
Usual items include:
Chromatogram- this is the graph that shows all the peaks from the GC trace
Peak Table- this chart lists each of the peaks that you integrated, the retention time, and the relative amounts
Spectrum graph- each spectrum graph will be a MS from a particular point in time. In the properties box you will need to pick the "spectrum" tab, change the "spectrum process table" to "retention time" and enter the retention time of the compound you are interested in. This may come from values in the peak table, or from the values you jotted down when you were doing your initial exploration of the data. The spectrum will show up better when printed if you also change the "line width" from 1 to 2.
Mass Table- sometimes you might need a listing of every ion in a particular mass spectrum. In the properties window, you will need to indicate the retention time for the MS you wish to display. Changing the "blocks" from 1 to 2 or 3 will have the data placed in 2 or 3 columns so that it will all possibly fit on the page. Sometimes you must start a new report to fit all this data on a page.