Apologies for answering your question with questions...

Have you got access to Auger Electron Spectroscopy (AES) or X-ray Photoelectron Spectroscopy (XPS)? Alternatively, do you have the facility to evacuate your FTIR apparatus?

In the former case, you should be able to detect very small surface concentrations. In both cases, you would minimise signals from atmospheric species.

I would believe detecting a monolayer via FTIR would be difficult. Have you thought of using XPS? Doing a narrow scan around 400 eV will show the chemical states of nitrogen (primary, secondary...).

Additionally, if possible, I had to purge the FTIR with nitrogen to get rid of any water or carbon dioxide signals.

I do not have access to any vacuum techniques including AES or XPS. I do not have the facilities to evacuate the FTIR since I am doing the measurement in reflective mode since the layer is on a gold layer (and gold reflects very well in the MIR region I am using). There is the ability to evacuate the spectrometer chamber, but that is only useful if the IR beam can travel through the sample to the in house detector. I am actually using a detector on a separate microscope which I am using to focus onto the surface of analysis.

Good point David - He and Ar should also be viable purge gases.

The most cost-effective solution would then probably be to create a purge chamber between the instrument and the detector you are using. The materials would be cheap and, providing you have a method of venting the purge gas safely (and an O2 sensor if safety considerations require such), the implementation should be fairly simple.

Feel free to attach a picture of your setup if you would like to discuss this further.

As much as this may be worth and you probably already know, but it appears that you have an XPS at Iowa State University, http://www.mrc.iastate.edu/facilities.htm

David, I appreciate the research! I do know that we have an XPS available on campus, but it will take to long for my sample to be analyzed (due to extensive use of the instrument by the group who owns it). I have a hard deadline coming up soon, so this instrument is out of the question as of right now.

I know this is past due, but for your info maybe fluorescein isothiocyanate would work, it's both reactive towards free amines and also is fluorescent.

Thank you David! I really appreciate the help. I had come across this, and I think I will try it out. My only concern is that the gold surface may reduce the fluorescence signal. I will get back on and let you know what happens after I test out the procedure.