Marwa Hussein I totally disagree with you that non-protein nitrogen is part of the total protein. The name itself already says it clearly: non-protein!
This link might also help: https://en.wikipedia.org/wiki/Protein
If all amino acids were determined, then the sum of all of them is a very good approximation of the protein content.
Be aware that generally the protein content is calculated by determining the N content and then multiplying by a certain factor based on the average amino acid composition of proteins. So this might also deviate from the "real" value.
Next to that all analyses have their margin of uncertainty, so do not worry too much.
Actually, we generally analyze all components which have nitrogen
by Kjeldahl methods and we present as crude protein content of the diet. However, to determine the amino acid profile chromatographic methods and different analysis methods for urea content can be used.