Amino Acid Analysis Overview

Amino Acid Analysis

The analysis of free amino acids present in food samples, body fluids such as urine, serum and blood, amino acid hydrolysates, from proteins, or primary and secondary amines is an important, standardized method routinely performed in biochemical, medical and biological labs. It has been, and still is used for the accurate quantification and characterization of proteins and peptides, as well as recombinant gene products. It is considered the method of choice to determine the purity and chemical composition of a protein or peptide.

1.  Types of amino acid analysis

A.  Hydrolysate analysis

Composition studies:  Determination of amino acid content of proteins, peptides, foods, beverages, cosmetics, and others.
Quality control:          Verification of product composition

B. Physiological analysis

Nutrition studies:       Determination of free amino acid content in food supplements, and others.
Clinical assays:          Determination of amino acid content in serum, tissue, and other body fluids.

Amino acid analysis (AAA) is a method for breaking down a protein or peptide into its components (amino acids) and determining their identities and relative quantities of the freed amino acids. Absolute quantities of amino acids released from the protein or peptide can also be determined.

AAA can be used in combination with protein sequence analysis to verify if the total sequence of the protein in question has been determined. It also helps to identify modified amino acids like phosphor-tyrosine, the presence of amino acids modified with carbohydrates, if amino sugars are found, and others.

Knowledge of the number of methionines or tryptophanes present allows for the design of peptide mapping strategies employing enzymatic or chemical cleavage methods to generate a limited number of longer peptides. These peptides may then be sequenced and used for the design of primers. Knowledge of the number of Lys, Arg, Asp, and Glu residues allows one to select the most appropriate protease for further experiments.

Even today, AAA is still the most practical method for accurately quantifying amino acid, peptide and protein concentrations. Accurate measurements are essential for calculating extinction coefficients of proteins or to determine the turnover number for an enzyme. Although instrumentation performance has improved over the years, the basic concepts of amino acid analysis have not changed since Stein and Moore (1963) developed the original method based on ion exchange resins.

2. Sample preparation

The preparation of samples to be used in AAA can be a quite difficult but very important experimental step for a successful amino acid analysis. Contamination with other proteins, amino acids, and other molecular weight solutes that interfere with the analysis chemistry are the most serious. To get accurate results the purity of the sample is much more critical than for sequencing or mass analysis.

2.1. Contamination with traces of undesired proteins

In the case of proteins a 10% contamination of the desired protein with an undesired byproduct such as a different protein may render the data useless.

2.2. Low molecular weight compounds

Compounds containing primary or secondary amino groups are a very serious problem. They can be found in abundance in every laboratory and are difficult to completely eliminate. Tris and glycine are two good examples. Contamination is the major factor limiting increases in the sensitivity of analysis. The rule of thumb here is: the more steps used prior to analysis the more contamination one can pick up.

2.3. Non-amines

Non-amine compounds including many buffers, detergents, and inorganic salts, especially high salt concentrations may interfere with the analysis and need to be removed prior to analysis.

2.4. Sample treatment for physiological samples

Physiological samples need to be treated differently than proteins prior to loading on to the derivatizer unit. To avoid losses of labile amino acids present in the sample, keep sample solutions on ice and store in freezer below -20 ºC between use or better (if enough sample is at hand), prepare aliquots and store frozen in freezer prior to analysis.

2.4.1.  Precipitation of proteins with 5-sulfocalicylic acid (SSA)

Human urine, serum and rat brain tissue extracts are treated with sulfosalicylic acid to precipitate protein: 20 µl of 35% sulfosalicylic acid is added to 200 µl of each sample.  These solutions are vortexed and allowed to sit at room temperature at least 20 minutes before proceeding.  The samples are then spun in a microfuge for 2 minutes and the supernatants are collected.

2.4.2.  Hydrolysis of proteins and peptides

Collagen samples are hydrolyzed in 6 N HCl, 110 oC for 24 hours.  The hydrolysates are then dried down and resuspended in 250 µg/ml K4EDTA or a different volume as needed. 
Ant hemolymph does not need to be pretreated before analysis.

Samples are loaded onto the analyzer as follows:  Urine - 10 µl of a 1:2 dilution of the supernatant, Serum - 10 µl of undiluted supernatant, Rat brain extract - 10 µl of the undiluted supernatant, Collagen hydrolysate - 1.2 µg in 15 µl,  Fire ant hemolymph - 4 µl of a 1:9 or 1:10 dilution.

Our current knowledge that approximately 30,000 human genes appear to code for up to 1 million or more proteins has generated new interest in independent ‘de novo’ protein and peptide sequencing of gene products. Two methods are available for this task, the classical Edman chemistry based method, or the newer, more recent method which utilizes LC-MS/MS based sequencing. The second method is considered to be faster and more sensitive.

When sufficient quantities are at hand, samples may be desalted by dialysis or size exclusion chromatography using deionized water or a volatile buffer like 1 N acetic acid. These two methods are not recommended to be used for quantities below 1 nanomole. Reversed phase-HPLC may be used for smaller sample quantities. But even this method can be tricky.

3. Hydrolysis methods

The second part of the analysis is the hydrolysis process. Many methods have been investigated to ensure optimal recoveries for the different amino acids analyzed.

3a. Standard hydrolysis conditions are 6N HCl from 20 to 96 hours at 110 ºC in vacuo.

Limitations and recovery improving modifications of the method are listed below:

  •  A single hydrolysis cannot yield quantitative recoveries for all amino acids present in the sample.
  •  Losses of up to 50-100% can be experienced for some amino acids.
  •  Adding reductants and/or scavengers to the hydrolysis acid will improve yields of amino acids sensitive to hydrolysis
         conditions (ser, thr, met, tyr).
  •  Shorter hydrolysis times and/or lower hydrolysis temperatures will improve yields of amino acids sensitive to hydrolysis 
               conditions but may obscure others.

3b. Hydrolysis of sensitive amino acids

Serine and threonine

Side chain hydroxyl group is modified during hydrolysis (eg. esterification, dehydration). Typical losses using standard hydrolysis conditions are 15-20% for serine and 10-15% for threonine.

A typical method for quantitation is to run multiple hydrolyses at different hydrolysis times and plot the serine and threonine recovery versus length of hydrolysis (hydrolyzed for 30, 60 and 90 min). Extrapolate the recovery to time = 0 to yield an accurate quantitation.

•   Tyrosine

Typical losses are 15-20% during hydrolysis (actual losses may be higher depending on the quality of acid used and sample amount). Side chain phenol group is attacked by traces of hypochlorite/chlorine free radicals present in HCl. The addition of scavengers is necessary to protect tyrosine. Typically phenol is added to the acid (0.1 to 1% by weight). The quality of the phenol is important. Poor quality phenol will not protect tyrosine.

  •  Methionine

Losses of methionine can vary depending on sample amount, quality of HCl, amount of oxygen present in the hydrolysis vessel, length of time the hydrolyzed sample is exposed to air on the sample slide etc. Side chain thioether is oxidized forming methionine sulfone and sulfoxide.

Addition of a reductant/scavenger improves methionine yields. Choice of reductants needs to be done carefully. Some reductants (thioglycolic acid, DTT, 2-mercapto-ethanol) react with PITC through their free sulfhydryl group and generate peaks that can interfere with the PTC-amino acid analysis. Borane-DIEA should not be used with the hydrolyzer.

  •  Cysteine/Cystine

Losses can be 50% or greater. The free sulfhydryl and disulfide groups are sensitive to a variety of side reactions during hydrolysis.

It is necessary to reduce the disulfide bonds and alkylate or oxidize the free sulfhydryl groups generated. Derivatization to form pyridylethyl or carboxy-methyl cysteine or oxidation to cysteic acid are typical techniques to quantitate this amino acid. One recommended technique is derivatization using 4-vinyl pyridine to form pyridylethyl cysteine.

  •  Tryptophan

Tryptophan is mostly destroyed during hydrolysis by attack on the carbon double bond in the indole ring.

It is not possible to get quantitative recovery of tryptophan from samples using acid hydrolysis. In manual hydrolysis the addition of thioglycolic acid to the acid (5-15% by volume) has given 70% recovery of trp at 500 pmol. Thioglycolic acid does generate a large interfering artifact peak in the PTC-chemistry. A method using dodecanthiol as a scavenger has proven to be useful.

  •  Asparagine and Glutamine

Quantitatively recovered as aspartic and glutamic acid respectively.

Many attempts have been made over the years to improve recoveries of hydrolysis sensitive amino acids as well as to generate overall quantitative recoveries for all studied amino acids. A collection of hydrolysis conditions studied is listed in table 1.

Table 1:   Protein/Peptide Hydrolysis Methods


Method & comments



 1.  Standard method

 6N HCl, 110 oC, 24-96h in vacuo


 2. improved Trp, Cys, Thr, Ser, Tyr recovery

 6N HCl +/- Phenol, 110oC, 20-24h in   vacuo, 150oC, 1-4 h in vacuo

 Moore & Stein (1963)

 3. improved Met, Cys, Tyr recovery

 6N HCL-Na2SO3, 110oC, 24h in vacuo

 Swadesh et al. (1984)

 4. improved Trp, Cys, Thr, Ser, Tyr recovery

 HCl/Propionic acid (1:1); 150 - 160oC 15 min, 130oC, 2h in vacuo

 Westall & Hesser (1974)

 5. improved Trp, Cys, Thr, Ser, Tyr recovery

 HCl/TFA (2:1), 166ºC 25 min in vacuo

 Tsugita & Scheffler (1982)

 6. improved Trp, Cys, Thr, Ser, Tyr recovery

 HCl/TFA (2:1), 5% (v/v) thioglycolic acid, 166ºC, 25 min in vacuo

 Yokote, et al., (1986)

 7. improved Trp, recovery

 6 N HCl, 0.5-6% (v/v) thioglycolic acid, 110oC, 24-64h in vacuo

 Matsubara & Sasaki (1969)

 8. improved Trp, recovery

 3N p-Toluenesulphonic acid, 110oC 24-72 h in vacuo


 Lui & Chang (1971)

 9. improved Trp, recovery

 3N Mercaptoethanesulfonic acid, 110oC 24-72 h in vacuo

 Penke et al., (1980)

 10. Phosphoamino acids  



 O-phospho-Ser, Thr & Tyr

1-3 N NaOH, 37-50oC 3-18 h; or 6N HCl 2 h and 4 h, respectively at 110oC, 1 h, 110oC,
 6N HCl or 5N KOH 155oC for 30 min

 6 N HCl, 110oC, 1-4 h

 Kemp (1980)

 Martensen (1982)

 Capony & Demaille (1983)


4. Derivatization methods for the amino acid analysis of proteins and peptides

Many pre-column derivatization chemistries have been investigated over the years. All of them suffer from major disadvantages such as incompatibility with aqueous samples or dissolved salts, or interference from reagent peaks in the analysis chromatogram. A list of derivatization methods commonly used is shown in the next table:

Table 2:     Derivatization Chemistries for Amino Acids and Amine Analysis



Detection mode

 1.   PITC


Pre-column derivatization,

 2.   OPA


Pre-column derivatization,
fluorescent and chemiluminescent detection

 3.    FMOC-Cl

fluorenyl methyl chloroformate

Pre-column derivatization,
fluorescent and chemiluminescent detection

 4.    OPA/FMOC-Cl combined


Pre-column derivatization,
fluorescent and chemiluminescent detection

 5.   DABS

4-dimethylaminoazo-benzene-4-sulfonyl (dabsyl) chloride

Pre-column derivatization,
detection: visible light

 6.   AQC, AccQ•Tag

6-aminoquinolyl-N-hydroxy-succinimidyl carbamate

Pre-column derivatization, fluorescent detection

 7.   Ninhydrin

Ruhemans purple

Post-column derivatization,

visible light (440 and 570 nm).


A "pre-column" derivatization method used by amino acid analyzer systems typically consists of several steps as listed below:

 1. Derivatization of amino acids
 2. Separation of derivatized amino acids by reversed phase chromatography
 3. Detection in UV or using fluorescence for increased sensitivity (some chemistries).

A "post-column" derivatization method mainly used for on-line ninhydrin derivatization in an automated amino acid analyzer consists of several steps as listed below:

 1. Separation of amino acids by ion exchange chromatography
 2. Derivatization of amino acids with ninhydrin at an elevated temperature
 3. Detection of derivatives via absorption in the visible range (440 and 570 nm).

The ninhydrin based system has been the most widely used system.

4.1. Derivatization of free amino acids using phenylisothiocyanate (PITC)

Figure 1: Derivatization reaction of amines and free amino acids using PITC.

PITC reacts with the free amino groups in amines and amino acids to form the phenylthiourea adduct of these compounds making them suitable for UV-detection. This reaction is used in the automated hydrolyzer/derivatizer set-up with on-line HPLC separation of the resulting PTC-amino acids and UV detection. Detection is done at 268 to 270 nm.

4.2 Derivatization of free amino acids using ortho-phthalaldehyde (OPA)

Figure 2: Derivatization reaction of amines and free amino acids using ortho-phthalaldehyde (OPA).

OPA reacts with the free amino groups in amines and amino acids in the presents of a reducing reagent like b-mercaptoethanol to form their isoindole-derivatieves making them suitable for UV-and fluorescence detection. This reaction is usually used in a pre-column derivatization step with an automated derivatizer set-up with on-line HPLC separation. UV detection is done at 338 nm. Fluorescence detection is done using excitation settings at 340 nm and emission settings at 450 nm.

4.3. Derivatization of free amino acids using (FMOC-Cl)

Figure 3: Derivatization reaction of amines and free amino acids using 9-fluorenylmethyl-chloroformat (Fmoc).

Fmoc reacts with the free amino groups in amines and amino acids to form Fmoc-derivatives making them suitable for UV-and fluorescence detection. This reaction is usually used in a pre-column derivatization step with an automated derivatizer set-up with on-line HPLC separation. UV detection is done at 262 nm. Fluorescence detection is done using excitation settings at 266 nm and emission settings at 305 nm.

4.4. Derivatization using Waters AccQ•TagTM amino acid analysis system

Figure 4A: AQC

(6-aminoquinolyl-N-hydroxy-succinimidyl carbamate. Chemical structure (left) and energy minimized molecular model (right). Calculations were done using the MNDO module from CACHE Scientific.

Figure 4B: Derivatization Chemistry.  

Both 1º and 2° amino acids and amines react rapidly with AQC to produce highly stable, fluorescent derivatives. The excess reagent reacts with water to form a free amine having significantly different fluorescence spectral properties.


Barkholt, V. and Jensen, A., Anal. Biochem., (1989) 177, 318-322.

Betner, I./ Foldi, P. New Automated Amino Acid Analysis by HPLC Precolumns Derivatization with Fluorenylmethyloxycarbonylchloride. Chromatographia Vol. 22, No. 7-12, Dec. 1986 -OPA/FMOC

Capony and Demaille, Anal. Biochem. 152, 206-212 (1983).

Carlson, R./ Srinivasachar, K./ Givens, R./ Matuszewski, B. New Derivatizing Agents fore Amino Acids and Peptides. 1. Facile Synthesis of N-Substituted 1-Cyanobenz[f]isoindoles and their Spectroscopic Properties. American Chemical Society (1986) 51, pg. 3978. -NDA

Chan, King/ Janini, George/ Muschik, Gary/ Issaq, Haleem.  Laser-induced fluorescence detectin of 9-fluorenylmethyl chloroformate derivatized amino acids in capillary electrophoresis.  Journal of Chromatography A, 653 (1993) 93-97 -OPA/FMOC-Cl/NDA

Cohen, Phillip/ Hubbard, Michael.  On target with a new mechanism for the regulation of protein phosphorylation.  TIBS 18, May 1993 pgs. 172-177.

Cohen, S. and Michaud, D., Anal. Biochem., (1993)

Cohen, s., and Strydom, D., Anal. Biochem., (1988) 174, 1-16.

Cohen, Steven/ Tarvin, Thomas/ Bidlingmeyer, Brian.Analysis of amino acids using precolumn derivatization with phenylisothiocyanate.American  Laboratory Aug 1984. -PITC

D'Aniello, Antimo/ Petrucelli, Leonard/ Gardner, Christina/ Fisher, George.  Improved Method for Hydrolyzing Proteins and Peptides without Inducing Racemization and for Determining Their True D-Amino Acid Content.  Analytical Biochemistry 213, 290-295 (1993)

Hancock, Diane/ Reeder, Dennis.  Analysis and configuration assignments of the amino acids in a pyroverdine-type siderophore by reversed-phase high-performance liquid chromatography.  Journal of Chromatography, 646 (1993) 335-343.  -PITC

Hariharan, M./ Naga, Sundar/ VanNoord, Ted. Systematic approach to the development of plasma amino acid analysis by high-performance liquid chromatography with ultraviolet detection with precolumn derivatization using phenyl isothiocyanate.  Journal of Chromatography, 621 (1993) pgs. 15-22. -PITC

Janssen, P./ van Nispen,J./ Melgers, P./ van den Bogaart, H./ Hamelinck, R./ Goverde, B. HPLC Analysis of Phenylthiocarbamyl (PTC) Amino Acids. I. Application in the Analysis of (Poly)peptides.  Chromatographia Vol. 22, No. &-12, pg. 351-357, Dec. 1986. -PITC

Jonge, Leon/ Breuer, Michel.  Modification of the analysis of amino acids in pig plasma.  Journal of Chromatography B, 6542 (1994) 90-96. 

Kawasaki , Takao/ Higuchi, Takeru/ Imai, Kazuhiro/ Wong, Osborne.  Determination of Dopamine, Norepinephrine, and Related Trace Amines by Prochromatographic Derivatization with Naphthalene-2,3-dicarboxaldehyde. Analytical Biochemistry 180, 279-285 (1989) -NDA-CN

Kemp, B.E. (1980) Relative alkali stability of some peptide o-phosphoserine and o-phosphothreonine esters.  FEBS Lett. 110, 308-312.

LeFevre, Joseph.  Reversed-phase thin-layer chromatographic separations of enantiomers of dansyl-amino acids using B-cyclodextrin as a moblie phase additive.  Journal of Chromatography A, 653 (1993) 293-302

Liu, T.-Y. and Chang, Y.H. (1971) Hydrolysis of proteins with p-toluenesulphonic acid. Determination of tryptophan. J. Biol. Chem.  246, 2842-2848.

Lobell, Mario/ Schneider, Manfred.  2,3,4,6-Tetra-O-benzoyl-B-D-glucopyranosyl isothiocyanate:an efficient reagent for the determination of enantiomeric purities of amino acids, B-adrenergic blockers and alkyloxiranes by high-performance liquid chromatography using standard reversed-phase columns.  Journal of Chromatography, 633 (1993) 287-294. AGIT

Lunte, Susan. Naphthalenedialdehyde-cyanide:A versatile fluorogenic reagent for the LC analysis of peptides and other primary amines.  >LC-GC Vol. 7, No. 11 pg. 908-916 -NDA-CN

Lunte, Susan/ Mohabbat, Tariq/ Wong, Osborne/ Kuwana, Theodore. Determinatin of Desmosine Idodesmosine, and Other Amino Acids by Liquid Chromatography with Electrochemical Detection following Precolumn Derivatization with Naphthalenedialedhyde/Cyanide.  Analytical Biochemistry 178, 202-207 (1989) -NDA

Martensen, T.M.  (1982) Phosphotyrosine in proteins.  Stability  and quantification.  J. Biol. Chem. 257, 9648-9652.

Matsubara & Sasaki, BBRC 35, 175-181 (1969).

Matuszewski, Bogdan/ Givens, Richards/ Srinivasachar, Kasturi/ Carlson, Robert/ Higuchi, Takeru.  N-Substituted 1-Cyanobenz[f]isoindole: Evaluation of Fluoresence Efficiencies of a New Fluorogenic Label for Primary Amines and Amino Acids.  Analytical Chemistry, Vol. 59, Page 1102, (1987) -NDA-CN

Montigny, Pierre/ Stobaugh, John/ Givens, Richard/ Carlson, Robert/ Srinivasachar, Kasturi/ Sternson, Larry/ Higuchi, Takeru.  Naphthalene-2,3-dicarboxaldehyde/Cyanide Ion: A Rationally Designed Fluorogenic Reagent for Primary Amines.  Analytical Chemistry (1987) Vol. 59, pg. 1096. -NDA-CN

Moore, S. and Stein, W.H. (1951) J. Biol. Chem. 178, 53-77.

Moore, S. and Stein, W.H. (1954) J. Biol. Chem. 211, 893-906.

Moore, S. and Stein, W.H. (1963) Methods Enzymol. 6, 819-831 (1963).

Neidle, Amos/ Banay-Schwartz, Miriam/ Sacks, Shirley/ Dunlop, David.  Amino Acid Analysis Using 1-Napthylisocyanate as a Precolumn High Performance Liquid Chroamatography Derivatization Reagent.  Analytical Biochemistry 189 (1989) 291-297. -PITC/ OPA/ FMOC-Cl

Nimura, N., Iwaki, K., Kinoshita, T., Takeda, K. and Ogura, H. (1986) Anal. Chem. 58, 2372-2375.

Organon, Janssen.  PTC-Amino Acid separation: C18 column.  Chromatographia, 22: 345-357 (1986) -PTC

Penke et al., Anal. Biochem. 60, 45-50 (1974).

Roach, Marc/ Harmony, Marlin.  Determination of Amino Acids at Subfemtomole Levels by High-Performance Liquid Chromatography with Laser-Induced Fluorescence Detection.  Analytical Chemistry, 1987, vol. 59 pg. 411.  -OPA

Slater, George/ Manville, John.  Analysis of thiocyanates and isothiocyanates by ammonia chemical ionization gas chromatography-mass spectrometry and gas chromatography-Fourier transform infrared spectroscopy.  Journal of Chromatography, 648 (1993) 433-443 -ITC

Strydom, D., and Cohen, S., in  Techniques in Protein Chemistry IV (R.H. Angeletti, ed.), Academic Press, (1993) San Diego

Strydom, D., Tarr, G., Pan, Y-C and Paxton, R., in  Techniques in Protein Chemistry II (R.H. Angeletti, ed.), Academic Press, (1992) San Diego , pp. 261-274.

Swadesh, J.K., Thannhauser, T.W., an Scheraga, H.A. (1984)  Sodium sulphite as an antioxidant in the acid hydrolysis of bovine pancreatic ribonuclease A. Anal. Biochem. 171, 133-123, 397-401 ibid?

Tsugita & Scheffler, Eur. J. Biochem. 124, 585-588 (1982).

vanEijk, Hans/ Rooyakkers, Dennis/ Deutz, Nicolaas.  Rapid routine determination of amino acids in plasma by high performance liquid chromatography with a 2-3 mm Spherisorb ODS II column.  Journal of Chromatography, 620 (1993) 143-148. - OPA

Waldron, Karen/ Dovichi, Norman. Sub-Femtomole Determination of Phenylthiohydantion-Amino Acids:  Capillary Electrophoresis and Thermooptical Detection.  Anal. Chem. (1992) 64, 1396-1399 -?

Westall & Hesser, Anal. Biochem. 61, 610-613 (1974).

Woo, Kang-Lyung/ Chang, Duk-Kyu.  Determination of 22 protein amino acids as N(O)-tert-butyldimethylsiyl derivatives by gas chromatography. Journal of Chromatography, 638 (1993) 97-107.

Wu, Guoyao. Determination of proline by reversed-phase high-performance liquid chromatography with automated pre-column o-phthaldialdehyde.  Journal of Chromatography, 641 (1993) 168-175  -OPA

Yokote, et al., Anal. Biochem. 152, 245-249 (1986).

Zhou, F./ Krull, I.  Solid-phase derivatization of amino acids and peptides in high-performance liquid chromatography.  Journal of Chromatography, 648 (1993) 357-365. -FMOC-Cl.