The Earth's atmosphere absorbs and reddens light from astronomical sources. The effect is dependent upon many factors: weather, observing site, time of year, time of day (or night), and so on. The process is known as atmospheric extinction. The depth of atmosphere through which an object is observed is another factor determining the extinction. This depth is known as air mass.
When an object lies at the zenith the depth of atmosphere through which it is observed is one air mass. As the zenith angle of the object increases, so does the air mass.
The effect of extinction is wavelength-dependent and so a table of correction factors is required. Each observatory should have such a table available for its site.
You should observe your standard star through as similar an air mass to the target as possible. Unless the standard is very close to the target, and both are at a fairly high altitude, you may still need to compensate for differential extinction, rather than simply assuming the atmosphere has the same effect on both observations. It may be a good strategy to observe your standards at a range of different altitudes throughout a night, then fit a curve to these and interpolate to calibrate the science observations.
If you are fortunate, the air mass for a particular observation will automatically be present in the FITS headers of your data - otherwise you will have to calculate it.
Simple Spectroscopy Reductions