sometimes arise, due to many rezones like physical rezones when you start to measure your sample , without scan background, environmental effect and power fluctuation .some times you may change in software programming like change ads -trans .
First of all let us know you are doing FTIR analysis using %T mode or ABS mode??secondly peak inversion may only happen if you have'nt operated the instrument or software according to its SOP like, first you need to scan back ground and then shifting the analysis mode to sample...if you didnt shift the mode, you may experiance invesrted peaks....i hope this may help you.
The inverted display of absorption, compared with UV-Visible spectra, is characteristic. Thus a sample that did not absorb at all would record a horizontal line at 100% transmittance (top of the chart)
I think, he meant only a few peaks are inverted the rest are not. I have exactly the same issue with my latest FTIR-ATR. I know it is an operational error since the first one was good (not inverted) but all following showed inverted peaks of the component with the lowest concentration.
@John Kabuba: Where is the problem? I only see one inverted peak related to CO2, which is pretty standard, as the CO2-concentration usually fluctuates during measurements in an open chamber.
Test the instrument parameters and purge N2 once, take proper background after each sample. Also due to CO2 , but some time main peaks also get inverted.
what i know , If you are scanning in Transmittance mode those inverted peaks will show you in which range it is absorbing that is which types of bonds are there .