Protein Beyond the Numbers: How Quality Impacts Nutrition

By Guy H. Johnson, PhD

The importance of protein for providing energy and meeting basic physiological needs for growth and other metabolic activity is well recognized.¹ Protein has also been shown to support increased muscle mass and function in healthy adults² and to provide satiety and suppress appetite.³ The 2025-2030 Dietary Guidelines for Americans⁴ underscores the importance of protein in a healthy diet, highlighting that many individuals may benefit from intakes above the longstanding 0.8 g/kg/day, with emerging guidance suggesting a range of 1.2–1.6 g/kg/day, adjusting as needed based on your individual caloric requirements.

Both the quantity and the quality of protein in the diet are important for the maintenance of optimal health. Protein quality is determined by two major considerations: the extent to which the indispensable (essential) amino acid content of the protein matches human physiological need, and its digestibility. The three methods commonly used to determine protein quality are summarized below:

The Protein Digestibility-Corrected Amino Acid Score (PDCAAS)

The Protein Digestibility-Corrected Amino Acid Score (PDCAAS) was adopted in 1991 by a joint FAO/WHO expert consultation⁵ as the preferred method for evaluating protein quality for human nutrition. It remains the regulatory basis for protein claims in the U.S. under FDA regulations.

PDCAAS combines:

The amino acid composition of a protein.
A comparison to a reference amino acid requirement pattern.
True fecal digestibility of the protein.

The score is calculated by identifying the first limiting indispensable amino acid (IAA) relative to human requirements and adjusting that ratio by overall protein digestibility. Scores are truncated at 1.00 (100%). The percent Daily Value(%DV) of protein per serving is calculated by multiplying the uncorrected %DV/serving by the PDCAAS value.

Despite its widespread use, PDCAAS has several recognized limitations:

Fecal digestibility is used rather than ileal digestibility, which potentially overestimates amino acid availability.
Truncation at 1.00 masks differences among high-quality proteins.
It does not assess digestibility of individual amino acids.

Hughes et al. noted that soy protein is the only widely available source of plant protein that has been shown to be a complete protein based on numerous nitrogen balance studies using isolated soy protein or soy protein concentrate.⁶Nevertheless, PDCAAS scores are subject to analytical variation. These researchers reported that three samples of isolated soy protein and one sample of soy protein concentrate had truncated scores of 1.00 when analyzed by one laboratory, but the same samples of isolated soy protein received scores of 0.95 to 0.98 when analyzed by a second laboratory. The authors noted that the application of amino acid nitrogen recovery factors was able to explain the differences. It was concluded that soy protein is a high-quality protein, comparable to meat, eggs, and dairy products.

Digestible Indispensable Amino Acid Score (DIAAS)

The Digestible Indispensable Amino Acid Score (DIAAS) was introduced by FAO in 2013⁷ to propose an alternative to PDCAAS. Unlike PDCAAS, DIAAS:

Uses ileal digestibility (amino acids measured at the end of the small intestine), which more precisely reflects the availability of amino acids for absorption.
Does not truncate higher scores, so that scores above 100 can be differentiated. This approach allows a protein that provides more digestible essential amino acids than the reference requirement to be identified.

DIAAS is calculated by comparing the digestible amount of each indispensable amino acid in a test protein to a reference amino acid requirement pattern. The lowest ratio (the limiting amino acid) determines the DIAAS value. If a protein delivers digestible amino acids in amounts that exceed requirements across the board, the DIAAS can exceed 100.

DIAAS values for soy protein ingredients and soy foods tend to be somewhat lower than PDCAAS values but still high relative to many plant proteins.⁸ A recent comprehensive review⁹ found that mean DIAAS across various soy products was ~84.5, with variability across product forms (tofu, soymilk, isolate, etc.). The mean PDCAAS score for these soy forms was only slightly higher at 85.6. The authors concluded that the majority of soy products have high protein quality scores, and that processing and post-processing conditions can increase or decrease protein quality.

Given limitations of the PDCAAS system, the DIAAS approach may more accurately reflect how well a protein meets human indispensable amino acid needs. Nevertheless, while DIAAS is influential in scientific and policy discussions globally, it is not currently used for regulatory purposes in the U.S. due to a variety of factors including limited human ileal digestibility data, reliance on growing pig models as proxies, as well as cost and feasibility of testing.Optimal application of this method may be in foods for special dietary uses, such as infant formula, and in contexts where a high level of rigor is necessary, including nutrition research. Broad application within regulatory frameworks for general foods intended for the overall population may not be warranted.

Indicator Amino Acid Oxidation (IAAO)

As noted above, PDCAAS and DIAAS assess protein quality relative to established reference amino acid requirement patterns. The Indicator Amino Acid Oxidation (IAAO) method helps establish human protein requirements, which can then be used alongside score metrics like PDCAAS or DIAAS to judge whether protein intakes from soy and other sources truly meet metabolic needs.¹⁰

The IAAO method measures oxidation of a labeled “indicator” amino acid (often L-[1-¹³C] phenylalanine) while varying intake of another indispensable test amino acid. Typically, subjects of interest (e.g., children, elderly) are provided with multiple test diets across separate study days that contain sufficient amounts of energy and all amino acids except the one being tested (e.g., methionine). The experimental diets differ in the amount of the test amino acid (i.e., low, medium, and high). The labeled indicator amino acid is administered to the subjects after each test diet has been consumed, and its oxidation rate is measured (e.g., by determining the amount of ¹³C in breath). When the test amino acid is insufficient, oxidation of the indicator amino acid increases. When the requirement is met, oxidation plateaus.¹¹

The IAAO method is based on the following conditions as described by Matsumoto et al.¹²

The oxidation of all amino acids will be substantial when amino acids other than the indicator amino acid are limited in the diet.
The oxidation of the indicator amino acid will decrease with increased dietary amino acid intake.
Upon meeting dietary requirements, the oxidation of the indicator amino acid will not change, and the resulting “breakpoint” will become the daily dietary protein requirement.

Humayun et al.¹³concluded the metabolic activity of total sulfur-containing amino acids from casein (87%) was slightly greater than that from soy protein isolate (72%) using the IAAO method in adult men. The differences in the metabolic availability of the total sulfur amino acids (TSAA) in casein and soy protein isolate are probably related to two important factors: 1) lower digestibility of methionine and cysteine in soy protein isolate than casein, and 2) greater first-pass splanchnic uptake and oxidation of sulfur amino acids from soy protein isolate. Nevertheless, van den Berg et al.⁹ reported that the majority of soy protein sources have high protein quality based on PDCAAS and DIAAS and that the effect of processing on such quality can be positive or negative. Furthermore, Humayun et al.¹³ concluded that more information on the optimal period of dietary adaptation to the intact test proteins and the influence of free versus protein-bound amino acids is needed before the IAAO technique can be widely applied to determine metabolic availability within a dietary protein.

Nutrition Labeling and Claims

The importance of protein quality is reflected in the U.S. nutrition labeling regulations. Protein is the only nutrient that must be adjusted for nutritional quality when calculating its %DV per serving. The Nutrition Labeling and Education Act specifies that essentially all products must declare grams of protein per serving, but declaration of the %DV is voluntary unless the product is intended for children under 4 years of age or a claim (e.g., “good/excellent source”) is made. As noted above, such values must be adjusted using the PDCAAS system.

At the same time, the International Food Information Council (IFIC) April 2026 survey on Americans’ Perceptions of Protein & Protein Labeling¹⁴suggests that key components of protein quality, such as essential amino acid composition and digestibility, are not actively used in shopper decision making. Instead, consumers tend to rely on more visible and accessible cues, including grams of protein, front-of-pack claims, and ingredient familiarity. While these can be helpful signals, they do not fully capture differences in protein quality, highlighting a disconnect between how protein is evaluated scientifically and how it is interpreted in practice.

Conclusion

PDCAAS, DIAAS, and IAAO each contribute to the scientific understanding of protein nutrition. PDCAAS remains the regulatory standard in the U.S. and supports soy’s classification as a high-quality protein. DIAAS provides a more refined scientific framework, though implementation challenges persist. IAAO advances knowledge of human amino acid requirements and may influence future scoring systems.

However, a clear disconnect remains between how protein quality is defined in the scientific community and how consumers evaluate the healthfulness of foods. While these methods assess factors such as amino acid composition and digestibility, there is an opportunity to more effectively translate the science so that evidence-based measures of protein quality are communicated in ways that align with how consumers choose, purchase, and consume food.

REFERENCES

Institute of Medicine. Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein and Amino Acids. Washington, DC: The National Academy Press; 2005.
Nunes EA, Colenso-Semple L, McKellar SR, et al. Systematic review and meta-analysis of protein intake to support muscle mass and function in healthy adults. J Cachexia Sarcopenia Muscle2022;13:795-810.
Kohanmoo A, Faghih S, Akhlaghi M. Effect of short- and long-term protein consumption on appetite and appetite-regulating gastrointestinal hormones, a systematic review and meta-analysis of randomized controlled trials. Physiology & Behavior 2020;226:113123.
U.S. Department of Agriculture and U.S. Department of Health and Human Services. 2025-2030 Dietary Guidelines for Americans. 2025.
FAO/WHO. Protein Quality Evaluation; Food and Agricultural Organization of the United Nations. Rome, Italy1991.
Hughes GJ, Ryan DJ, Mukherjea R, Schasteen CS. Protein digestibility-corrected amino acid scores (PDCAAS) for soy protein isolates and concentrate: criteria for evaluation. J Agric Food Chem. 2011 Dec 14;59(23):12707-12. doi: 10.1021/jf203220v. Epub 2011 Nov 16. PMID: 22017752. https://pubmed.ncbi.nlm.nih.gov/22017752/
Dietary protein quality evaluation in human nutrition. Report of an FAQ Expert Consultation. FAO Food Nutr Pap 2013;92:1-66.
Rutherfurd SM, Fanning AC, Miller BJ, Moughan PJ. Protein Digestibility-Corrected Amino Acid Scores and Digestible Indispensable Amino Acid Scores Differentially Describe Protein Quality in Growing Male Rats1, 2,3. The Journal of Nutrition 2015;145:372-
Van den Berg LA, Mes JJ, Mensink M, Wanders AJ. Protein quality of soy and the effect of processing: A quantitative review. Front Nutr 2022;9:1004754.
Elango R, Ball RO, Pencharz PB. Indicator amino acid oxidation: concept and application. JNutr 2008;138:243-6.
Malowany JM, van Lieshout GAA, Verdijk LB, Moore DR, van Loon LJC, Trommelen J. The indicator amino acid oxidation (IAAO) technique: a novel approach to assess protein intakes that maximize whole-body protein anabolism. Crit Rev Food Sci Nutr 2026;66:1172-81.
Matsumoto M, Narumi-Hyakutake A, Kakutani Y, et al. Evaluation of protein requirements using the indicator amino acid oxidation method: a scoping review. The Journal of Nutrition 2023;153:3472-89.
Humayun MA, Elango R, Moehn S, Ball RO, Pencharz PB. Application of the indicator amino acid oxidation technique for the determination of metabolic availability of sulfur amino acids from casein versus soy protein isolate in adult men. J Nutr 2007;137:1874-9.
International Food Information Council Spotlight Survey: Americans’ Perceptions Of Protein Quality & Labeling. April, 2026. Available at: https://ific.org/research/perceptions-protein-quality-labeling/.

PROTEIN BEYOND THE NUMBERS: HOW QUALITY IMPACTS NUTRITION

REFERENCES

ABOUT THE AUTHOR: