4 things to remember about Amino Acid Analysis of proteins & peptides

Amino Acid analysis
Sep 23. 2016

Why perform Amino Acid Analysis?

Amino acid analysis of proteins is a method to determine the absolute amounts of individual amino acids in a sample. The technique is applicable for samples containing free amino acids. However, it is also helpful for peptides and protein samples after hydrolysis into amino acids [1, 2].

AA analysis can determine the relative composition of amino acids in a protein. Determining the absolute amount of a protein or peptide is also recommended if the amino acid sequence is known. In addition, it is a crucial part of the extinction coefficient determination of a protein or antibody of interest. Finally, the analysis is ideal for the purity estimation of a purified protein [3].

We recommend that you determine the protein concentration of your sample before host cell protein analysis and other quantitative analyses. It aids in calculating the appropriate sample volume for protein digestion and preparation for mass spectrometry-based workflows, thus resulting in more accurate and valuable data.

When using amino acid analysis, you should note that:

  1. Serine and threonine degrade slightly during acid hydrolysis, and recoveries are sometimes up to 10% lower than expected.
  2. Methionine can oxidize during hydrolysis; however, less than 10% is usually oxidized.
  3. Valine and isoleucine bonds (Val-Val, Ile-Val, Val-Ile, Ile-Ile) are challenging to hydrolyze, and recoveries are often 5-15% lower than expected.
  4. Glycine content is often higher than expected because it is a frequent contaminant from many buffers. Determining a compensation factor to correct for differences in ninhydrin reactivity uses an analysis of known amounts of AA standards. [1-3].

Hopefully, you now have a good idea of what to observe when performing amino acid analysis. If you need more information, you may want to visit this page to read more about Amino Acid quantification >>>

Related blog posts on amino acid analysis:

I highly recommend that you spend some time familiarizing yourself with the information in these blog posts:

Important reasons why you need to determine the concentration of your protein standards accurately >>

How to determine the Molar Extinction Coefficient of protein in 3 small steps >>

Biochrom amino acid analyzer


[1]          Rutherfurd et al.: “Amino acid analysis, “Current Protocols in Protein Science2009

[2]          Rutherfurd et al.: “Quantitative amino acid analysis, “Current Protocols in Protein Science2011

[3]          Noble et al.: “Quantification of protein, “Methods in Enzymology2009

More posts about Analysis of Amino Acid in protein
  • 4 things to remember about Amino Acid Analysis of proteins & peptides

  • Determine the Molar Extinction Coefficient of protein in 3 small steps

  • Why you need accurate concentration determination of protein standards

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