Protein sources are routinely described as complete, high quality or inferior, and those descriptions come from formal scoring systems. The systems do not agree, and the disagreement is methodological.
Quality means amino acid pattern relative to requirement
The body cannot synthesize certain amino acids, so a protein's usefulness depends on whether it supplies those in proportions matching what the body needs to build its own proteins.
A scoring system compares the amino acid profile of a food against a reference pattern derived from estimated human requirements, which themselves differ by age.
The amino acid present in the smallest proportion relative to the reference limits how much of the protein can be used, and that limiting amino acid sets the score.
Digestibility corrects the raw profile
An amino acid present in a food is only useful if it is absorbed, so scores multiply the amino acid comparison by a digestibility factor.
Plant sources frequently carry fiber, phytates and cell wall structures that reduce the fraction absorbed, so their corrected scores fall further than their raw profiles suggest.
Processing changes this. Cooking, milling, soaking and fermentation all raise digestibility, which means a score attached to a raw ingredient may not describe the food as eaten.
The two main systems measure at different points
An older and widely used system measures digestibility across the whole digestive tract, comparing what enters the mouth against what leaves the body.
The difficulty is that gut bacteria in the large intestine consume and produce amino acids, so what exits does not cleanly reflect what the body absorbed.
A newer system measures at the end of the small intestine instead, where absorption actually happens, and scores each amino acid separately rather than only the limiting one.
Ceilings and combinations distort comparisons
The older system truncates scores at a maximum, so several high-quality proteins share an identical top value and cannot be distinguished from one another.
Truncation was intended to prevent a very high-quality protein from appearing to compensate for a poor one in a mixed diet, but it removes information.
Combining sources also changes the outcome, since a food limited in one amino acid pairs usefully with a food limited in a different one across the day.
What a score does not tell a reader
Scores rank protein against a reference for building tissue. They say nothing about the rest of the food, its fat profile, its fiber or its place in a pattern of eating.
Protein needs shift with age, activity, pregnancy and kidney function, and anyone with reduced kidney function in particular has requirements that must be set by a clinician rather than inferred from a ranking table.