You don't see the vibrations, or are they shifted? The molecules are quite different so probably when you perform you data collection what you are seeing is a shift in the position, aren't you? Another thing that could be happening is that those peaks are not enhanced by you Ag particles as the 4ATP are. There are just too many variables that without knowing more about the system makes it harder to answer. :/

Since you're doing the Raman measurement on silver particles, the natural question that comes to mind is, do you see those two peaks for both molecules when  you measure them neat?  (wanted to check if you're trying to do SERS)

If you can do FTIR measurements on your samples and compare the FTIR and Raman data, then it may help you to understand the behavior of your samples.  Sometimes you may not see a Raman signal where you normally might expect to see them if the symmetry is altered due to sample processing and changes in the sample structure.   This may change the vibrational characteristics so a Raman active mode disappears, but at the same time an IR forbidden mode appears in the FTIR spectra, indicating a change in the symmetry and not a chemical change.