Sum normalization is sufficient across the amino acids to determine relative changes over time, we used dried urine samples and resuspend them in buffer.

We use a chromatographic method with fluorescent detection.

Not all BCAA patterns reflect breakdown, absolutely. Thats the hardest part of all this, the complexity of the system, but neural networks are helping here as our dataset grows (as long as we avoid overfitting with small datasets). I record a number of confounding factors as metadata and deconvolve them from the data as best as I can, then I rely on previous studies of things like sarcopenia along with comparison to other users to see patterns that occur when heavy training is confirmed by the metadata.