Amino acids are small organic molecules that make up peptides and proteins. All living organisms share the same set of amino acids. Amino acids come together in different orders (sequences) to form proteins. As such, each type of protein has a different three-dimensional structure and biological activity.
Protein sequencing is a method that typically utilizes mass spectrometry (MS) to determine the amino acid code of a protein1. Prior to the development of mass spectrometry, Edman degradation, a method involving the stepwise degradation of peptides to derive the order of amino acids, was the mainstream approach. Nowadays, mass spectrometry is favored due to its ease of use and high throughput capabilities, though Edman degradation is still employed for specific applications in which the technique is well suited.
Amino acids (aa)—the building blocks of proteins—are simple molecules characterized by a variable R group flanked either side by an amino group and a carboxyl group. With around 20 different commonly found amino acids, each one can bond with another to produce chains that can be classified as peptides (typically below 50 aa) and proteins (sequences above 50 aa)—molecules ubiquitous to every known organism.
Amino acid sequencing is commonly performed using Edman degradation or mass spectrometry (MS). While mass spectrometry is favoured for its high throughput capabilities and ease of use, both techniques possess their own features and limitations. This article summarizes some of the key pain points inherent in the two methodologies when determining the amino acid sequence.
Written by Yuning Wang, PhD August 1, 2021 What is DNA Sequencing? DNA sequencing is the process of determining the precise order of four nucleotides bases—adenine (A), guanine (G), cytosine (C), and thymine (T)—that make up the DNA molecule. From Sanger sequencing to next-generation sequencing (NGS), DNA sequencing’s accessibility and ease [...]
Proteins are composed of peptide chains, which in turn are made up of a string or linear sequence of amino acids (Figure 1A). Every amino acid has a basic structure containing an amino (-NH2) group and a carboxylic (-COOH) group (Figure 1B). To form a peptide, amino acids link to each other via a peptide bond, which involves the reaction between the carboxylic group of one amino acid and the amine group of another amino acid (Figure 1B). As such, the primary structure of a protein is typically recorded starting at the amino-terminal (N) end and continuing to the carboxyl-terminal (C) end. The primary protein structure may be directly sequenced from a sample of the protein itself or inferred from the DNA sequence.
Protein mass spectrometry refers to the use of mass spectrometry in the study and characterization of proteins, including their quantification, profiling, interaction mapping, and identification of their post-translational modifications (1,2). Protein mass spectrometry may also be referred to as mass spectrometry-based proteomics. Mass spectrometry-based proteomics consist of three approaches: top-down, middle-down, and bottom-up proteomics
Amino acid sequencing is the process of identifying the arrangement of amino acids in proteins and peptides. Numerous distinct amino acids have been discovered in nature but all proteins in the human body are comprised of just twenty different types.
Nowadays, DNA sequencing is so popular that it is easy to forget that the first sequenced biological material was protein – insulin, by Sanger. Sanger, and another researcher, Edman, separately pioneered protein sequencing.
One of the most important pieces of information researchers need to know during early stage antibody drug research and development is the sequence information of the antibody protein. With the advancement of mass spectrometry instrumentation and technologies, it is helpful, and sometimes critical, to conduct sequence analysis using mass spectrometry experiments.