Normally calculating peak areas in a GC-MS chromatogram can be done automatically or manually through the data analysis software. Exactly how this is done will vary with different manufacturers' software. In Agilent systems you will find the integrate function under the chromatogram tab on the top tool bar. If you then click on integrate the software will automatically integrate all peaks above a set area in your chromatogram. You can change the minimum peak area, type of integration etc from the same tab. To get the results you click on integration results which brings up a table of results which can be copied and pasted into Excel. Manual integration, where you integrate only the peaks you want, can be found under Tools > options - then choose manual integration. This allows you to draw a line across the base of the peak you wish to know the area of using a right mouse click and holding down while you draw.

MZMine as MS data processing tool or export and further processing with Origin are other options in addition to those mentioned by Valerie.

Dear_!

You can find area of a peak by pressing "i" and left button of mouse and drag cursor at the base of the peak which cover full peak base. which will directly give you area.