Subtract the background. Every instrument has its own measurement characteristics that change with time, temperature, and ambient environment. Take a measurement with nothing in the sample compartment and store that as the background. The spectrometer will automatically subtract the background from subsequent measurements.

Use the internal calibration source. Many FTIR spectrometers have an internal fixed-spectrum source used for internal calibrations. The internal calibration routine will automatically determine any corrections and apply them to the detector output.

Insert a calibration standard into the sample compartment and acquire a measurement. The calibration standard is a known compound with a known concentration. Ideally, your calibration standard will have spectral features in the same region as your unknown. Consult the National Institute of Standards and Technology for information as well as the actual gas, liquid, or solid standard reference materials (SRMs).

Repeat the previous step with samples of different concentrations. You will want to cover the range of possible concentrations of your sample.

Do a regression analysis to develop an equation representing the detector response as a function of calibration standard concentration. For example, your measurements will show something like this: your detector measures 70 counts at a certain wave number when the concentration is 100 parts per million (ppm), 40 counts at 200 ppm, and 10 counts at 300 ppm. A regression analysis would show that the number of counts is 100 - 0.3 * concentration in ppm. In practice, this will all be done by the same software package you use to analyze your data.