Can you measure an IR spectrum of a sample inside a glass vial?
As EdV said, when you have aqueous samples, Raman spectroscopy is the way to go. The problem is not the container (which should not be glass etc),the problem is water. Its absorption will hide the absorption of everything.
If you ever open an FTIR instruments, you will see that there is nothing which is made of glass or quartz because they absorb too strongly in the useful IR range.