Role of Acetonitrile and Ammonium Acetate buffer in Leucomalachite Green stock solution?
Since they're using ACN/ammonium acetate to elute from solid phase extraction cartridges and that's what they're injecting into their LC analysis, they probably want to use the same mixture to avoid problems with unmatched matrices with their standards. The ammonium acetate is the pH buffer. Malachite green has different protonation states at different pH, so it's important to set the pH properly for elution from the SPE and LC analysis. MG is fairly soluble in water, but still has a lot of organic functionality, so adding an organic solvent would help elute from the SPE column and keep the analyte from being too strongly retained by the LC stationary phase.

As for raman analysis, water has rather weak raman scattering, so it's not usually a problem. Acetonitrile has one very strong peak at 2942 $\mathrm{cm^{-1}}$ and a few moderate peaks, so it might be an issue. Since you're not doing LC, you can likely prepare standards in buffer only. Unfortunately, ammonium acetate is also raman-active, but if you're not doing LC, you might be able to do without as well. Fortunately, one of the great powers of IR and raman spectroscopies is that there is often enough bandwidth to find one or two non-overlapping peaks in a complex mixture and use that for quantitation, so it may still work as written. They're both also very amenable to chemometric techniques like partial least squares when measuring complex samples.

The big problem is going to be sensitivity if you're interested in the concentrations they use in the paper.. Normal raman is not that sensitive and the smallest standard is only ~3 nM, so it's probably going to be hopeless. These guys do surface-enhaced resonance raman and are able to get to about 1 nM, and the raman setup's not actually that hard since MG has a huge absorbance at 620 nm, right where HeNe lasers emit. Unfortunately, MG doesn't fluoresce much in solution or it would be very easy to measure.