I made some ethanolic extracts, but I don't know which are the factors (temperature, pH) involved in vanillin degradation that may alter those samples before HPLC analysis.
If you sonicate or give ultrasound exposure to vanillin casein,or casein powder at 20 kHz no measurable changes may occur in free vanillin content that could be detected in ultracentrifuged. But a small, temporary decrease in pH may result from sonication; similarly, no measurable change may occur in soluble ions. Sonication may change viscosity . Controlled application of ultrasound can be usefully applied to reverse process-induced protein aggregation without affecting the native state of casein micelles if sonicated. In HPLC there may be effect on resultion factor of peaks, and all sonicated molecules may form smear and a falling cumulative peak may appear, or smaller sized peaks may arise from the base, that can shift the peak displaying vanillin.